CPAD 2.0

Entry	PDB ID	Protein Name	Species	Length	Mutation(s)	Class	Type	Method	Resolution (Å)	PMID
S-0361	4OMO	Proto-oncogene tyrosine-protein kinase Src	Gallus gallus	61	Q128E	Amyloid	Protein	X-RAY DIFFRACTION	1.04	25490095
S-0362	4OMP	Proto-oncogene tyrosine-protein kinase Src	Gallus gallus	76	Q128K	Non-amyloid	Protein	X-RAY DIFFRACTION	2.0	25490095
S-0363	4ONF	Amyloid-Beta		222 , 219 , 7	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.0	25024748
S-0364	4ONG	Amyloid-Beta		222 , 219 , 40	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.2	25024748
S-0365	4ONK	Enkephalin mutant	synthetic construct	5	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.9	24915112
S-0366	4P4V	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.97	25915729
S-0367	4P4W	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.5	25915729
S-0368	4P4X	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.9	25915729
S-0369	4P4Y	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.51	25915729
S-0370	4P4Z	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.31	25915729
S-0371	4WC8	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.9080000000000001	25915729
S-0372	4X0S	Beta-2-Microglobulin	synthetic construct	16	No	Amyloid	Fibril	X-RAY DIFFRACTION	2.032	25915729
S-0373	4Q8D	Amyloid-Beta		18	No	Non-amyloid	Peptide	X-RAY DIFFRACTION	1.75	25068693
S-0374	4QXX	Bone marrow proteoglycan	Homo sapiens	5	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.45	25728769
S-0375	4QYA	Transthyretin	Homo sapiens	127	V30M	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.7	26020516
S-0376	4QXV	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.12	26020516
S-0377	4R0F	Lysozyme C	Gallus gallus	129	No	Amyloid	Protein	X-RAY DIFFRACTION	1.94	26926993
S-0378	4R0P	Lysozyme C	Homo sapiens	6	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.52	25474758
S-0379	4R0U	Alpha-synuclein	Homo sapiens	7	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.38	25474758
S-0380	4R0W	Alpha-synuclein	Homo sapiens	7	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.5	25474758
S-0381	4R9H	Beta-2-microglobulin	Homo sapiens	100	S33C	Amyloid	Protein	X-RAY DIFFRACTION	1.9	26420657
S-0382	4RA3	Beta-2-microglobulin	Homo sapiens	100	S33C	Amyloid	Aggregating complex	X-RAY DIFFRACTION	2.8	26420657
S-0383	4RAH	Beta-2-microglobulin	Homo sapiens	100	S33C	Amyloid	Protein	X-RAY DIFFRACTION	1.4	26420657
S-0384	4RAV	Huntingtin		126 , 117 , 126 , 117 , 17 , 17	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.5	25861763
S-0385	4RIK	Alpha-synuclein	Homo sapiens	9	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.85	26352473
S-0386	4RIL	Alpha-synuclein	Homo sapiens	11	No	Amyloid	Fibril	ELECTRON CRYSTALLOGRAPHY	1.43	26352473
S-0387	4RP6	Cellular tumor antigen p53	Homo sapiens	7	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.7	26748848
S-0388	4RP7	Cellular tumor antigen p53	Homo sapiens	6	No	Amyloid	Fibril	X-RAY DIFFRACTION	1.58	26748848
S-0389	4TKW	Transthyretin	Homo sapiens	125	L55P	Amyloid	Protein	X-RAY DIFFRACTION	1.8	26459562
S-0390	4TL4	Transthyretin	Homo sapiens	125	V30M	Amyloid	Protein	X-RAY DIFFRACTION	1.75	26459562

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

S

H

M

T

F

V

A

L

Y

D

Y

E

S

R

T

E

T

D

L

S

F

K

G

25

26

E

R

L

Q

I

V

N

T

E

G

D

W

L

A

H

S

L

T

G

E

T

G

50

51

Y

I

P

S

N

Y

V

A

P

S

D

61

Chain 2

1

G

S

H

M

T

F

V

A

L

Y

D

Y

E

S

R

T

E

T

D

L

S

F

K

G

25

26

E

R

L

Q

I

V

N

T

E

G

D

W

L

A

H

S

L

T

G

E

T

G

50

51

Y

I

P

S

N

Y

V

A

P

S

D

61

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of the c-Src tyrosine kinase SH3 domain mutant Q128E; The Gln128Glu mutant forms amyloid fibrils at neutral pH but not at mild acid pH

They have solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6?22 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P2?2?2?, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. The residue at position 128 is connected to Glu106 at the diverging Beta-turn through a cluster of water molecules.

Literature

PMID:	25490095
Author(s):	Bacarizo, J., Martinez-Rodriguez, S., Martin-Garcia, J.M., Andujar-Sanchez, M., Ortiz-Salmeron, E., Neira, J.L., Camara-Artigas, A.
Reference:	PLoS One. 2014 Dec 9;9(12):e113224.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Proto-oncogene tyrosine-protein kinase Src
Alternative Name:	Proto-oncogene c-Src, pp60c-src
Gene Name:	SRC
Sequence Length:	61
Species:	Gallus gallus
Mutation(s):	Q128E
E.C. Number:	2.7.10.2
UniProt ID:	P00523
Keyword(s):	Proto-oncogene tyrosine-protein kinase Src

Structure Information

PDB ID:	4OMO
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Monomer - A
PDB Classification:	TRANSFERASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.04
R free:	0.168

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
EPE	A	C8 H18 N2 O4 S	238.3	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID	C1CN(CCN1CCO)CCS(=O)(=O)O	JKMHFZQWWAIEOD-UHFFFAOYSA-N
NI	A	Ni 2	58.69	NICKEL (II) ION	[Ni+2]	VEQPNABPJHWNSG-UHFFFAOYSA-N
NI	B	Ni 2	58.69	NICKEL (II) ION	[Ni+2]	VEQPNABPJHWNSG-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

G

S

H

S

G

L

V

P

R

G

S

H

M

T

F

V

A

25

26

L

Y

D

Y

E

S

R

T

E

T

D

L

S

F

K

G

E

R

L

Q

I

V

N

50

51

T

E

G

D

W

L

A

H

S

L

T

G

K

T

G

Y

I

P

S

N

Y

V

A

75

76

P

76

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of the intertwined dimer of the c-Src tyrosine kinase SH3 domain mutant Q128K

They have solved the crystallographic structures of the wild-type (WT) and Gln128Glu, Gln128Lys and Gln128Arg mutants from crystals obtained at different pHs. At pH 5.0, crystals belong to the hexagonal space group P6?22 and the asymmetric unit is formed by one chain of the protomer of the c-Src-SH3 domain in an open conformation. At pH 7.0, crystals belong to the orthorhombic space group P2?2?2?, with two molecules at the asymmetric unit showing the characteristic fold of the SH3 domain. The residue at position 128 is connected to Glu106 at the diverging Beta-turn through a cluster of water molecules.

Literature

PMID:	25490095
Author(s):	Bacarizo, J., Martinez-Rodriguez, S., Martin-Garcia, J.M., Andujar-Sanchez, M., Ortiz-Salmeron, E., Neira, J.L., Camara-Artigas, A.
Reference:	PLoS One. 2014 Dec 9;9(12):e113224.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Proto-oncogene tyrosine-protein kinase Src
Alternative Name:	Proto-oncogene c-Src, pp60c-src
Gene Name:	SRC
Sequence Length:	76
Species:	Gallus gallus
Mutation(s):	Q128K
E.C. Number:	2.7.10.2
UniProt ID:	P00523
Keyword(s):	Proto-oncogene tyrosine-protein kinase Src

Structure Information

PDB ID:	4OMP
Amyloid Category:	Non-amyloid
Type:	Protein
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	TRANSFERASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.0
R free:	0.261

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
PEG	A	C4 H10 O3	106.12	DI(HYDROXYETHYL)ETHER	C(COCCO)O	MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGE	A	C6 H14 O4	150.17	TRIETHYLENE GLYCOL	C(COCCOCCO)O	ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

E

V

K

L

V

E

S

G

L

V

K

P

G

A

S

L

K

L

S

C

A

S

25

26

G

F

T

F

S

N

Y

G

M

S

W

V

R

Q

N

S

D

K

R

L

E

W

V

A

S

50

51

I

R

S

G

R

T

Y

S

D

N

V

K

G

R

F

T

I

S

R

E

N

A

75

76

K

N

T

L

Y

L

Q

M

S

L

K

S

E

D

T

A

L

Y

C

V

R

Y

D

100

101

H

Y

S

G

S

D

Y

W

G

Q

G

T

V

T

V

S

A

K

T

P

125

126

S

V

Y

P

L

A

P

G

S

A

Q

T

N

S

M

V

T

L

G

C

L

V

K

G

150

151

Y

F

P

E

P

V

T

V

T

W

N

S

G

S

L

S

G

V

H

T

F

P

A

V

175

176

L

Q

S

D

L

Y

T

L

S

V

T

V

P

S

T

W

P

S

E

T

V

T

200

201

C

N

V

A

H

P

A

S

T

K

V

D

K

I

V

P

R

D

C

G

222

Chain 2

1

Y

V

M

T

Q

T

P

L

T

L

S

V

T

I

G

Q

P

A

S

I

S

C

K

S

25

26

S

Q

S

L

D

S

D

G

K

T

Y

L

N

W

L

Q

R

P

G

Q

S

P

K

50

51

R

L

I

Y

L

V

S

K

L

D

S

G

V

P

D

R

F

T

G

S

G

S

G

T

D

75

76

F

T

L

K

I

S

R

I

E

A

E

D

L

G

L

Y

C

W

Q

G

T

H

F

P

100

101

R

T

F

G

T

K

L

E

I

K

R

A

D

A

P

T

V

S

I

F

P

125

126

S

E

Q

L

T

S

G

A

S

V

C

F

L

N

F

Y

P

K

D

I

N

150

151

V

K

W

K

I

D

G

S

E

R

Q

N

G

V

L

N

S

W

T

D

Q

D

S

K

D

175

176

S

T

Y

S

M

S

T

L

T

L

T

K

D

E

Y

E

R

H

N

S

Y

T

C

E

200

201

A

T

H

K

T

S

T

S

P

I

V

K

S

F

N

R

N

E

C

219

Chain 3

1

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

F

A

E

D

V

G

25

26

S

N

K

G

A

I

G

L

M

V

G

V

40

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Fab fragment of 3D6 in complex with amyloid beta 1-40

Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-Beta1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide.

Literature

PMID:	25024748
Author(s):	Feinberg, H., Saldanha, J.W., Diep, L., Goel, A., Widom, A., Veldman, G.M., Weis, W.I., Schenk, D., Basi, G.S.
Reference:	Alzheimers Res Ther. 2014 Jun 2;6(3):31.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Amyloid-Beta
Alternative Name:	ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II
Gene Name:	APP, A4, AD1
Sequence Length:	222 , 219 , 40
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	4ONG
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Hetero 2-mer - AB
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.2
R free:	0.22699999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CL	H	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
IMD	H	C3 H5 N2 1	69.08	IMIDAZOLE	c1c[nH+]c[nH]1	RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	H	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	L	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
IMD	L	C3 H5 N2 1	69.08	IMIDAZOLE	c1c[nH+]c[nH]1	RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	L	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 2

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 3

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK; oligomer structure

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MAA)AVK

Structure Information

PDB ID:	4P4V
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.97
R free:	0.222

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CL	A	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	A	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	B	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	B	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	C	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	C	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 2

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 3

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 4

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 5

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 6

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 7

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 8

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 9

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 10

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 11

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Chain 12

1

A

Y

L

F

Y

T

E

A

K

V

A

V

A

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Dodecamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVA(MVA)AVK; oligomer structure

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MVA)AVK

Structure Information

PDB ID:	4P4W
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 12-mer - A12
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.5
R free:	0.209

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MVA	A	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MVA	B	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
CL	C	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MVA	C	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	D	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	D	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MVA	E	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	E	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MVA	F	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	F	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MVA	G	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	G	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	G	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	H	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
nan	H	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN	H	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	H	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	H	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MVA	I	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	I	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	I	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
CL	J	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MVA	J	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	J	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	J	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	J	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	K	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MVA	K	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	K	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	K	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	L	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	L	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	L	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	L	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 2

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 3

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 4

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 5

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 6

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 7

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 8

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 9

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 10

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 11

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 12

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Dodecamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVA(MLE)AVK; oligomer structure

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	CYCLIC HEXADECAPEPTIDE (ORN)YLL(PH7)YTE(ORN)KVA(MLE)AVK

Structure Information

PDB ID:	4P4X
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 12-mer - A12
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.235

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MLE	A	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MLE	B	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MLE	C	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	C	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MLE	D	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MLE	E	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	E	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MLE	F	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MLE	G	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	G	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	G	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	G	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MLE	H	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	H	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	H	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MLE	I	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	I	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	I	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MLE	J	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	J	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	J	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
CL	K	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MLE	K	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	K	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	K	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	K	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	L	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MLE	L	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	L	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	L	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Chain 2

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Chain 3

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Chain 4

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Chain 5

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Chain 6

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Chain 7

1

A

Y

L

F

Y

T

E

A

K

V

T

A

T

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK; oligomer structure

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK

Structure Information

PDB ID:	4P4Y
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.51
R free:	0.175

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MAA	A	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	B	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
CL	C	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	C	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MAA	D	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	D	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MAA	E	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MAA	F	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
CL	G	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	G	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	G	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	G	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 2

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 3

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 4

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 5

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 6

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 7

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 8

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 9

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 10

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 11

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Chain 12

1

A

Y

L

F

Y

T

E

A

K

V

T

V

T

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Octomer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK; oligomer structure

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK

Structure Information

PDB ID:	4P4Z
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 8-mer - A8
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.31
R free:	0.175

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MVA	A	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
PO4	A	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
MVA	B	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
nan	B	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
PO4	B	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
MVA	C	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	D	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
PO4	D	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
MVA	E	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
nan	E	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	F	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
PO4	F	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K
MVA	G	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	G	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	G	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	H	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
nan	H	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN	H	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	H	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	I	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	I	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	I	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	J	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	J	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	J	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	K	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	K	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	K	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MVA	L	C6 H13 N O2	131.17	N-METHYLVALINE	CC(C)[C@@H](C(=O)O)NC	AKCRVYNORCOYQT-YFKPBYRVSA-N
ORN	L	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	L	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
PO4	L	O4 P -3	94.97	PHOSPHATE ION	[O-]P(=O)([O-])[O-]	NBIIXXVUZAFLBC-UHFFFAOYSA-K

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 2

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 3

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 4

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 5

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 6

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 7

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 8

1

A

Y

L

F

Y

T

E

A

K

V

A

L

A

V

K

16

Chain 9

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 10

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 11

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Chain 12

1

A

Y

L

F

Y

T

E

A

K

V

A

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Heterogeneous dodecamer formed from macrocycles containing a sequence from beta-2-microglobulin(63-69).

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS

Structure Information

PDB ID:	4WC8
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 12-mer -Â A12
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9080000000000001
R free:	0.21899999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
MAA	A	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MLE	B	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MLE	C	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	C	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	C	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	C	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MLE	D	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	D	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	D	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
MAA	E	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	E	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	E	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	E	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MLE	F	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	F	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	F	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
CL	G	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MLE	G	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	G	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	G	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	G	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	H	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MLE	H	C7 H15 N O2	145.2	N-METHYLLEUCINE	CC(C)C[C@@H](C(=O)O)NC	XJODGRWDFZVTKW-LURJTMIESA-N
ORN	H	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	H	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	H	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	I	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	I	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	I	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	I	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	I	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MAA	J	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	J	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	J	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	J	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
CL	K	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	K	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	K	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	K	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	K	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
MAA	L	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
ORN	L	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	L	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Y

L

F

Y

V

E

A

K

V

A

V

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin.

[Oligomer structures rather than fibrils] They present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of Beta2-microglobulin (Beta2m). Each macrocyclic peptide contains the heptapeptide sequence Beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form Beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of Beta-sheets. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers.

Literature

PMID:	25915729
Author(s):	Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.
Reference:	J Am Chem Soc. 2015 May 20;137(19):6304-11.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-Microglobulin
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	synthetic construct
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	ORN-TYR-LEU-LEU-PHI-TYR-VAL-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS

Structure Information

PDB ID:	4X0S
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.032
R free:	0.20199999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CL	A	Cl -1	35.45	CHLORIDE ION	[Cl-]	VEXZGXHMUGYJMC-UHFFFAOYSA-M
MAA	A	C4 H9 N O2	103.12	N-methyl-L-alanine	C[C@@H](C(=O)O)NC	GDFAOVXKHJXLEI-VKHMYHEASA-N
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

A

Q

K

L

V

F

A

E

D

A

Q

K

L

V

X

E

D

18

Chain 2

1

A

Q

K

L

V

F

A

E

D

A

Q

K

L

V

X

E

D

18

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of a macrocyclic beta-sheet peptide containing two beta-strands from amyloid beta residues 15-23; A Fibril-Like Assembly of Oligomers of a Peptide Derived from beta-Amyloid.

A macrocyclic Beta-sheet peptide containing two nonapeptide segments based on ABeta(15-23) (QKLVFFAED) forms fibril-like assemblies of oligomers in the solid state. The X-ray crystallographic structure of macrocyclic Beta-sheet peptide 3 was determined at 1.75 A resolution. The macrocycle forms hydrogen-bonded dimers, which further assemble along the fibril axis in a fashion resembling a herringbone pattern. The extended Beta-sheet comprising the dimers is laminated against a second layer of dimers through hydrophobic interactions to form a fibril-like assembly that runs the length of the crystal lattice. The second layer is offset by one monomer subunit, so that the fibril-like assembly is composed of partially overlapping dimers, rather than discrete tetramers. In aqueous solution, macrocyclic Beta-sheet 3 and homologues 4 and 5 form discrete tetramers, rather than extended fibril-like assemblies.

Literature

PMID:	25068693
Author(s):	Pham, J.D., Spencer, R.K., Chen, K.H., Nowick, J.S.
Reference:	J Am Chem Soc. 2014 Sep 10;136(36):12682-90.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Amyloid-Beta
Alternative Name:
Gene Name:
Sequence Length:	18
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):	macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23

Structure Information

PDB ID:	4Q8D
Amyloid Category:	Non-amyloid
Type:	Peptide
Global Stoichiometry:
PDB Classification:	DE NOVO PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.75
R free:	0.22

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
HAO	A	C10 H11 N3 O5	253.21	{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid	COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O	GRLLMVZTTMERGI-UHFFFAOYSA-N
MPD	A	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	A	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	A	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N
HAO	B	C10 H11 N3 O5	253.21	{[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo)acetic acid	COc1ccc(cc1C(=O)NN)NC(=O)C(=O)O	GRLLMVZTTMERGI-UHFFFAOYSA-N
MPD	B	C6 H14 O2	118.17	(4S)-2-METHYL-2,4-PENTANEDIOL	C[C@@H](CC(C)(C)O)O	SVTBMSDMJJWYQN-YFKPBYRVSA-N
ORN	B	C5 H12 N2 O2	132.16	L-ornithine	C(C[C@@H](C(=O)O)N)CN	AHLPHDHHMVZTML-BYPYZUCNSA-N
PHI	B	C9 H10 I N O2	291.09	IODO-PHENYLALANINE	c1cc(ccc1C[C@@H](C(=O)O)N)I	PZNQZSRPDOEBMS-QMMMGPOBSA-N

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

M

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

M

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of human transthyretin variant V30M in complex with luteolin

They generated high-resolution crystal-structures of both TTR wild type and the amyloidogenic mutant V30M in complex with luteolin. The results show that the A-ring of luteolin, in contrast to what was previously suggested, is buried within the TBS, consequently explaining the lack of activity from cynaroside. The flavonoids represent an interesting group of drug candidates for TTR amyloidosis. The present investigation shows the potential of luteolin as a stabilizer of TTR in vivo.

Literature

PMID:	26020516
Author(s):	Iakovleva, I., Begum, A., Pokrzywa, M., Walfridsson, M., Sauer-Eriksson, A.E., Olofsson, A.
Reference:	PLoS One. 2015 May 28;10(5):e0128222.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	V30M
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	4QYA
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	TRANSPORT PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.7
R free:	0.198

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
LU2	A	C15 H10 O6	286.24	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one	c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O	IQPNAANSBPBGFQ-UHFFFAOYSA-N
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
LU2	B	C15 H10 O6	286.24	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one	c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O	IQPNAANSBPBGFQ-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

M

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

M

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

CRYSTAL STRUCTURE of HUMAN TRANSTHYRETIN IN COMPLEX WITH LUTEOLIN AT 1.1 A RESOLUTION

They generated high-resolution crystal-structures of both TTR wild type and the amyloidogenic mutant V30M in complex with luteolin. The results show that the A-ring of luteolin, in contrast to what was previously suggested, is buried within the TBS, consequently explaining the lack of activity from cynaroside. The flavonoids represent an interesting group of drug candidates for TTR amyloidosis. The present investigation shows the potential of luteolin as a stabilizer of TTR in vivo.

Literature

PMID:	26020516
Author(s):	Iakovleva, I., Begum, A., Pokrzywa, M., Walfridsson, M., Sauer-Eriksson, A.E., Olofsson, A.
Reference:	PLoS One. 2015 May 28;10(5):e0128222.

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	4QXV
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	TRANSPORT PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.12
R free:	0.133

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
GOL	A	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
LU2	A	C15 H10 O6	286.24	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one	c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O	IQPNAANSBPBGFQ-UHFFFAOYSA-N
nan	A	Na 1	22.99	SODIUM ION	[Na+]	FKNQFGJONOIPTF-UHFFFAOYSA-N
GOL	B	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N
LU2	B	C15 H10 O6	286.24	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one	c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O	IQPNAANSBPBGFQ-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Chain 2

1

K

V

F

G

R

C

E

L

A

M

K

R

H

G

L

D

N

Y

R

G

Y

S

L

25

26

G

N

W

V

C

A

K

F

E

S

N

F

N

T

Q

A

T

N

R

N

T

D

G

S

50

51

T

D

Y

G

I

L

Q

I

N

S

R

W

C

N

D

G

R

T

P

G

S

R

N

L

75

76

C

N

I

P

C

S

A

L

S

D

I

T

A

S

V

N

C

A

K

I

V

S

100

101

D

G

N

G

M

N

A

W

V

A

W

R

N

R

C

K

G

T

D

V

Q

A

W

I

R

125

126

G

C

R

L

129

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Structure of Lysozyme Dimer at 318K

They report results on how heat transforms globular protein, lysozyme into building block of Beta-amyloids. Light scattering experiments showed formation of lower order associated species around 50-70?Â°C followed by rapid cooperativity to Beta-amyloid fibrils. crystallization drops set at higher temperatures either led to aggregates or spherulites. The latter possess an amorphous Beta-fibril rich core with thin crystalline needles projecting outwards. Diffraction of the crystalline outgrowths revealed novel dimers and trimers of lysozyme where individual chains were similar to monomer with marginal gain in Beta-sheet content. Overall this work concludes that heat induced weakly associated structures of lysozyme are the first step towards its amyloid formation.

Literature

PMID:	26926993
Author(s):	Sharma, P., Verma, N., Singh, P.K., Korpole, S., Ashish
Reference:	Sci Rep. 2016 Mar 1;6:22475.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Lysozyme C
Alternative Name:	1, 4-beta-N-acetylmuramidase C, Allergen Gal d IV
Gene Name:	LYZ
Sequence Length:	129
Species:	Gallus gallus
Mutation(s):	No
E.C. Number:	3.2.1.17
UniProt ID:	P00698
Keyword(s):	Lysozyme C

Structure Information

PDB ID:	4R0F
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.94
R free:	0.239

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
GOL	A	C3 H8 O3	92.09	GLYCEROL	C(C(CO)O)O	PEDCQBHIVMGVHV-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

I

Q

R

T

P

K

I

Q

V

Y

S

R

H

P

A

E

N

G

K

S

N

F

L

N

25

26

C

Y

V

S

G

F

H

P

C

D

I

E

V

D

L

K

N

G

E

R

I

E

K

V

50

51

E

H

S

D

L

S

F

S

K

D

W

S

F

Y

L

Y

T

E

F

T

P

T

E

75

76

K

D

E

Y

A

C

R

V

N

H

V

T

L

S

Q

P

K

I

V

K

W

D

R

D

M

100

Chain 2

1

M

I

Q

R

T

P

K

I

Q

V

Y

S

R

H

P

A

E

N

G

K

S

N

F

L

N

25

26

C

Y

V

S

G

F

H

P

C

D

I

E

V

D

L

K

N

G

E

R

I

E

K

V

50

51

E

H

S

D

L

S

F

S

K

D

W

S

F

Y

L

Y

T

E

F

T

P

T

E

75

76

K

D

E

Y

A

C

R

V

N

H

V

T

L

S

Q

P

K

I

V

K

W

D

R

D

M

100

Chain 3

1

M

I

Q

R

T

P

K

I

Q

V

Y

S

R

H

P

A

E

N

G

K

S

N

F

L

N

25

26

C

Y

V

S

G

F

H

P

C

D

I

E

V

D

L

K

N

G

E

R

I

E

K

V

50

51

E

H

S

D

L

S

F

S

K

D

W

S

F

Y

L

Y

T

E

F

T

P

T

E

75

76

K

D

E

Y

A

C

R

V

N

H

V

T

L

S

Q

P

K

I

V

K

W

D

R

D

M

100

Chain 4

1

M

I

Q

R

T

P

K

I

Q

V

Y

S

R

H

P

A

E

N

G

K

S

N

F

L

N

25

26

C

Y

V

S

G

F

H

P

C

D

I

E

V

D

L

K

N

G

E

R

I

E

K

V

50

51

E

H

S

D

L

S

F

S

K

D

W

S

F

Y

L

Y

T

E

F

T

P

T

E

75

76

K

D

E

Y

A

C

R

V

N

H

V

T

L

S

Q

P

K

I

V

K

W

D

R

D

M

100

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of dimeric S33C beta-2 microglobulin mutant in complex with Thioflavin (ThT) at 2.8 Angstrom resolution

An intermolecular interaction between D strands of facing Beta2m molecules was repeatedly observed, suggesting that such interface may be relevant for Beta2m dimerization. By mutating Ser33 to Cys, and assembling the disulphide-stabilized Beta2m homodimer (DimC33), such DD strand interface was locked. Although the isolated DimC33 display a stability similar to wt Beta2m under native conditions, it shows enhanced amyloid aggregation propensity. Three distinct crystal structures of DimC33 suggest that dimerization through the DD interface is instrumental for enhancing DimC33 aggregation propensity. Furthermore, the crystal structure of DimC33 in complex with the amyloid-specific dye Thioflavin-T pinpoints a second interface, which likely participates in the first steps of Beta2m aggregation.

Literature

PMID:	26420657
Author(s):	Halabelian, L., Relini, A., Barbiroli, A., Penco, A., Bolognesi, M., Ricagno, S.
Reference:	Sci Rep. 2015 Sep 30;5:14651.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Beta-2-microglobulin
Alternative Name:
Gene Name:	B2M, CDABP0092, HDCMA22P
Sequence Length:	100
Species:	Homo sapiens
Mutation(s):	S33C
E.C. Number:
UniProt ID:	P61769
Keyword(s):	Beta-2-microglobulin

Structure Information

PDB ID:	4RA3
Amyloid Category:	Amyloid
Type:	Aggregating complex
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	IMMUNE SYSTEM
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.8
R free:	0.20600000

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
TFX	A	C17 H19 N2 S 1	283.41	2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium	Cc1ccc2c(c1)sc([n+]2C)c3ccc(cc3)N(C)C	FXEKRIDRIFBJOR-UHFFFAOYSA-N
TFX	B	C17 H19 N2 S 1	283.41	2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium	Cc1ccc2c(c1)sc([n+]2C)c3ccc(cc3)N(C)C	FXEKRIDRIFBJOR-UHFFFAOYSA-N
TFX	C	C17 H19 N2 S 1	283.41	2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium	Cc1ccc2c(c1)sc([n+]2C)c3ccc(cc3)N(C)C	FXEKRIDRIFBJOR-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

Q

V

Q

L

Q

E

S

G

L

V

Q

P

G

S

L

R

L

S

C

A

S

25

26

G

F

T

F

S

Y

S

M

S

W

V

R

Q

A

P

G

K

G

L

E

W

V

A

V

50

51

I

S

Y

D

G

S

N

K

Y

A

D

S

V

K

G

R

F

T

I

S

R

D

N

S

75

76

K

N

T

L

Y

L

Q

M

N

S

L

R

A

E

D

T

A

V

Y

C

A

R

D

R

100

101

Y

F

D

L

W

G

R

G

T

L

V

T

V

S

G

S

G

S

G

125

126

G

126

Chain 2

1

S

Q

S

A

L

T

Q

P

A

S

V

S

G

S

P

G

Q

S

I

T

I

S

C

T

G

25

26

T

S

D

I

G

A

Y

N

Y

V

S

W

Y

Q

Y

P

G

K

A

P

K

L

50

51

I

Y

D

V

S

N

R

P

S

G

I

S

N

R

F

S

G

S

K

S

G

D

T

A

S

75

76

L

T

I

S

G

L

Q

A

E

D

E

A

D

Y

C

S

F

A

N

S

G

P

L

100

101

F

G

T

K

V

T

V

L

G

H

117

Chain 3

1

Q

V

Q

L

Q

E

S

G

L

V

Q

P

G

S

L

R

L

S

C

A

S

25

26

G

F

T

F

S

Y

S

M

S

W

V

R

Q

A

P

G

K

G

L

E

W

V

A

V

50

51

I

S

Y

D

G

S

N

K

Y

A

D

S

V

K

G

R

F

T

I

S

R

D

N

S

75

76

K

N

T

L

Y

L

Q

M

N

S

L

R

A

E

D

T

A

V

Y

C

A

R

D

R

100

101

Y

F

D

L

W

G

R

G

T

L

V

T

V

S

G

S

G

S

G

125

126

G

126

Chain 4

1

S

Q

S

A

L

T

Q

P

A

S

V

S

G

S

P

G

Q

S

I

T

I

S

C

T

G

25

26

T

S

D

I

G

A

Y

N

Y

V

S

W

Y

Q

Y

P

G

K

A

P

K

L

50

51

I

Y

D

V

S

N

R

P

S

G

I

S

N

R

F

S

G

S

K

S

G

D

T

A

S

75

76

L

T

I

S

G

L

Q

A

E

D

E

A

D

Y

C

S

F

A

N

S

G

P

L

100

101

F

G

T

K

V

T

V

L

G

H

117

Chain 5

1

M

A

T

L

E

K

L

M

K

A

F

E

S

L

K

S

F

17

Chain 6

1

M

A

T

L

E

K

L

M

K

A

F

E

S

L

K

S

F

17

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of scFvC4 in complex with the first 17 AA of huntingtin

The C4 single-chain Fv antibody (scFv) binds to the first 17 residues of huntingtin [HTT(1-17)] and generates substantial protection against multiple phenotypic pathologies in situ and in vivo. They show that C4 scFv inhibits amyloid formation by exon1 fragments of huntingtin in vitro and elucidate the structural basis for this inhibition and protection by determining the crystal structure of the complex of C4 scFv and HTT(1-17). The peptide binds with residues 3-11 forming an amphipathic helix that makes contact with the antibody fragment in such a way that the hydrophobic face of this helix is shielded from the solvent. Residues 12-17 of the peptide are in an extended conformation and interact with the same region of another C4 scFv:HTT(1-17) complex in the asymmetric unit, resulting in a Beta-sheet interface within a dimeric C4 scFv:HTT(1-17) complex.

Literature

PMID:	25861763
Author(s):	De Genst, E., Chirgadze, D.Y., Klein, F.A., Butler, D.C., Matak-Vinkovic, D., Trottier, Y., Huston, J.S., Messer, A., Dobson, C.M.
Reference:	J Mol Biol. 2015 Jun 19;427(12):2166-78.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Huntingtin
Alternative Name:	Huntington disease protein
Gene Name:	HTT, HD, IT15
Sequence Length:	126 , 117 , 126 , 117 , 17 , 17
Species:
Mutation(s):	No
E.C. Number:
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	4RAV
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer -A4
PDB Classification:	IMMUNE SYSTEM/Apoptosis
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.5
R free:	0.226

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
SO4	B	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
SO4	C	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L
SO4	D	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

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Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

T

I

T

L

E

6

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Structure of the amyloid-forming segment TIITLE from p53 (residues 253-258)

They show that a cell-penetrating peptide, ReACp53, designed to inhibit p53 amyloid formation, rescues p53 function in cancer cell lines and in organoids derived from high-grade serous ovarian carcinomas (HGSOC), an aggressive cancer characterized by ubiquitous p53 mutations. Rescued p53 behaves similarly to its wild-type counterpart in regulating target genes, reducing cell proliferation and increasing cell death.

Literature

PMID:	26748848
Author(s):	Soragni, A., Janzen, D.M., Johnson, L.M., Lindgren, A.G., Thai-Quynh Nguyen, A., Tiourin, E., Soriaga, A.B., Lu, J., Jiang, L., Faull, K.F., Pellegrini, M., Memarzadeh, S., Eisenberg, D.S.
Reference:	Cancer Cell. 2016 Jan 11;29(1):90-103.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Cellular tumor antigen p53
Alternative Name:
Gene Name:
Sequence Length:	6
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P04637
Keyword(s):	TIITLE hexapeptide segment from p53

Structure Information

PDB ID:	4RP7
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 6-mer - A6
PDB Classification:	PROTEIN FIBRIL
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.58
R free:	0.192

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
ZN	Z	Zn 2	65.41	ZINC ION	[Zn+2]	PTFCDOFLOPIGGS-UHFFFAOYSA-N

Structure database of aggregation related proteins and peptides

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