{"method": "X-RAY DIFFRACTION", "mutation_s_field": "No", "ec_number": "", "description": "[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.", "ligstr": "MVA:A:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:A:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:A:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:A:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L;MVA:B:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:B:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:B:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;CL:C:Cl -1:35.45:CHLORIDE ION:[Cl-]:InChI=1S/ClH/h1H/p-1:VEXZGXHMUGYJMC-UHFFFAOYSA-M;MVA:C:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:C:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:C:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;MVA:D:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:D:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:D:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:D:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L;MVA:E:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:E:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:E:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:E:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L;CL:F:Cl -1:35.45:CHLORIDE ION:[Cl-]:InChI=1S/ClH/h1H/p-1:VEXZGXHMUGYJMC-UHFFFAOYSA-M;MVA:F:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:F:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:F:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:F:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L;CL:G:Cl -1:35.45:CHLORIDE ION:[Cl-]:InChI=1S/ClH/h1H/p-1:VEXZGXHMUGYJMC-UHFFFAOYSA-M;MVA:G:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:G:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:G:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;MVA:H:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;nan:H:Na 1:22.99:SODIUM ION:[Na+]:InChI=1S/Na/q+1:FKNQFGJONOIPTF-UHFFFAOYSA-N;ORN:H:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:H:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:H:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L;MVA:I:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:I:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:I:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;CL:J:Cl -1:35.45:CHLORIDE ION:[Cl-]:InChI=1S/ClH/h1H/p-1:VEXZGXHMUGYJMC-UHFFFAOYSA-M;MVA:J:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:J:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:J:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:J:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L;CL:K:Cl -1:35.45:CHLORIDE ION:[Cl-]:InChI=1S/ClH/h1H/p-1:VEXZGXHMUGYJMC-UHFFFAOYSA-M;MVA:K:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:K:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:K:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;MVA:L:C6 H13 N O2:131.17:N-METHYLVALINE:CC(C)[C@@H](C(=O)O)NC:InChI=1S/C6H13NO2/c1-4(2)5(7-3)6(8)9/h4-5,7H,1-3H3,(H,8,9)/t5-/m0/s1:AKCRVYNORCOYQT-YFKPBYRVSA-N;ORN:L:C5 H12 N2 O2:132.16:L-ornithine:C(C[C@@H](C(=O)O)N)CN:InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1:AHLPHDHHMVZTML-BYPYZUCNSA-N;PHI:L:C9 H10 I N O2:291.09:IODO-PHENYLALANINE:c1cc(ccc1C[C@@H](C(=O)O)N)I:InChI=1S/C9H10INO2/c10-7-3-1-6(2-4-7)5-8(11)9(12)13/h1-4,8H,5,11H2,(H,12,13)/t8-/m0/s1:PZNQZSRPDOEBMS-QMMMGPOBSA-N;SO4:L:O4 S -2:96.06:SULFATE ION:[O-]S(=O)(=O)[O-]:InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2:QAOWNCQODCNURD-UHFFFAOYSA-L", "pmid": "25915729", "remarks": "Dodecamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVA(MVA)AVK; oligomer structure", "amyloid_non_amyloid": "Amyloid", "type": "Fibril", "inchi": 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"resolution": "1.5", "species": "synthetic construct", "secondary_structure": "AYLLFYTEAKVAVAVK#CEEEEECCCCBEEEEC&AYLLFYTEAKVAVAVK#CEEEEECCCCBEEEEC&AYLLFYTEAKVAVAVK#CEEEEECCCCBEEEEC&AYLLFYTEAKVAVAVK#CEEEEECCCCBEEEEC&AYLLFYTEAKVAVAVK#CEEEEECCCCBEEEEC&AYLLFYTEAKVAVAVK#CEEEEEECCCEEEEEC&AYLLFYTEAKVAVAVK#CEEEEEECCCEEEEEC&AYLLFYTEAKVAVAVK#CEEEEEECCCEEEEEC&AYLLFYTEAKVAVAVK#CEEEEEECCCEEEEEC&AYLLFYTEAKVAVAVK#CEEEEEECCCEEEEEC&AYLLFYTEAKVAVAVK#CBEEEEECCCEEEEEC&AYLLFYTEAKVAVAVK#CEEEEEECCCEEEEEC", "chain_id": "A%%A%%A%%A%%B%%B%%B%%C%%C%%C%%C%%D%%D%%D%%D%%E%%E%%E%%E%%F%%F%%F%%F%%F%%G%%G%%G%%G%%H%%H%%H%%H%%H%%I%%I%%I%%J%%J%%J%%J%%J%%K%%K%%K%%K%%L%%L%%L%%L", "gene_names": "", "r_value_free": "0.209", "pdb_id": "4P4W", "reference": "J Am Chem Soc. 2015 May 20;137(19):6304-11.", "keyword": "CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVA(MVA)AVK", "protein_name": "Beta-2-Microglobulin", "ligand_formula": "C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%Cl -1%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2%%Cl -1%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2%%Cl -1%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%C6 H13 N O2%%Na 1%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%Cl -1%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2%%Cl -1%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%C6 H13 N O2%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2", "peptide_protein_sequence": "chain-ID A: AYLLFYTEAKVAVAVK; chain-ID B: AYLLFYTEAKVAVAVK; chain-ID C: AYLLFYTEAKVAVAVK; chain-ID D: AYLLFYTEAKVAVAVK; chain-ID E: AYLLFYTEAKVAVAVK; chain-ID F: AYLLFYTEAKVAVAVK; chain-ID G: AYLLFYTEAKVAVAVK; chain-ID H: AYLLFYTEAKVAVAVK; chain-ID I: AYLLFYTEAKVAVAVK; chain-ID J: AYLLFYTEAKVAVAVK; chain-ID K: AYLLFYTEAKVAVAVK; chain-ID L: AYLLFYTEAKVAVAVK", "entry": "S-0367", "length": "16", "uniprot_ac": "", "author": "Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.", "ligand_smiles": 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"ligand_mw": "131.17%%132.16%%291.09%%96.06%%131.17%%132.16%%291.09%%35.45%%131.17%%132.16%%291.09%%131.17%%132.16%%291.09%%96.06%%131.17%%132.16%%291.09%%96.06%%35.45%%131.17%%132.16%%291.09%%96.06%%35.45%%131.17%%132.16%%291.09%%131.17%%22.99%%132.16%%291.09%%96.06%%131.17%%132.16%%291.09%%35.45%%131.17%%132.16%%291.09%%96.06%%35.45%%131.17%%132.16%%291.09%%131.17%%132.16%%291.09%%96.06", "alternative_name": "", "ligand_name": "N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%SULFATE ION%%N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%CHLORIDE ION%%N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%SULFATE ION%%N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%SULFATE ION%%CHLORIDE ION%%N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%SULFATE ION%%CHLORIDE ION%%N-METHYLVALINE%%L-ornithine%%IODO-PHENYLALANINE%%N-METHYLVALINE%%SODIUM ION%%L-ornithine%%IODO-PHENYLALANINE%%SULFATE 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"ligand_id": "MVA%%ORN%%PHI%%SO4%%MVA%%ORN%%PHI%%CL%%MVA%%ORN%%PHI%%MVA%%ORN%%PHI%%SO4%%MVA%%ORN%%PHI%%SO4%%CL%%MVA%%ORN%%PHI%%SO4%%CL%%MVA%%ORN%%PHI%%MVA%%nan%%ORN%%PHI%%SO4%%MVA%%ORN%%PHI%%CL%%MVA%%ORN%%PHI%%SO4%%CL%%MVA%%ORN%%PHI%%MVA%%ORN%%PHI%%SO4"}