{"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": "CL:A:Cl -1:35.45:CHLORIDE ION:[Cl-]:InChI=1S/ClH/h1H/p-1:VEXZGXHMUGYJMC-UHFFFAOYSA-M;MAA:A:C4 H9 N O2:103.12:N-methyl-L-alanine:C[C@@H](C(=O)O)NC:InChI=1S/C4H9NO2/c1-3(5-2)4(6)7/h3,5H,1-2H3,(H,6,7)/t3-/m0/s1:GDFAOVXKHJXLEI-VKHMYHEASA-N;nan:A:Na 1:22.99:SODIUM ION:[Na+]:InChI=1S/Na/q+1:FKNQFGJONOIPTF-UHFFFAOYSA-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", "pmid": "25915729", "remarks": "X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin.", "amyloid_non_amyloid": "Amyloid", "type": "Fibril", "inchi": "InChI=1S/ClH/h1H/p-1%%InChI=1S/C4H9NO2/c1-3(5-2)4(6)7/h3,5H,1-2H3,(H,6,7)/t3-/m0/s1%%InChI=1S/Na/q+1%%InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1%%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%%InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2", "resolution": "2.032", "species": "synthetic construct", "secondary_structure": "AYLLFYVEAKVAAAVK#CCEEEEECCCEEEEEC", "chain_id": "A%%A%%A%%A%%A%%A", "gene_names": "", "r_value_free": "0.20199999", "pdb_id": "4X0S", "reference": "J Am Chem Soc. 2015 May 20;137(19):6304-11.", "keyword": "ORN-TYR-LEU-LEU-PHI-TYR-VAL-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS", "protein_name": "Beta-2-Microglobulin", "ligand_formula": "Cl -1%%C4 H9 N O2%%Na 1%%C5 H12 N2 O2%%C9 H10 I N O2%%O4 S -2", "peptide_protein_sequence": "chain-ID A: AYLLFYVEAKVAAAVK; chain-ID B: AYLLFYVEAKVAAAVK; chain-ID C: AYLLFYVEAKVAAAVK; chain-ID D: AYLLFYVEAKVAAAVK; chain-ID E: AYLLFYVEAKVAAAVK; chain-ID F: AYLLFYVEAKVAAAVK; chain-ID G: AYLLFYVEAKVAAAVK; chain-ID H: AYLLFYVEAKVAAAVK; chain-ID I: AYLLFYVEAKVAAAVK; chain-ID J: AYLLFYVEAKVAAAVK; chain-ID K: AYLLFYVEAKVAAAVK; chain-ID L: AYLLFYVEAKVAAAVK", "entry": "S-0372", "length": "16", "uniprot_ac": "", "author": "Spencer, R.K., Kreutzer, A.G., Salveson, P.J., Li, H., Nowick, J.S.", "ligand_smiles": "[Cl-]%%C[C@@H](C(=O)O)NC%%[Na+]%%C(C[C@@H](C(=O)O)N)CN%%c1cc(ccc1C[C@@H](C(=O)O)N)I%%[O-]S(=O)(=O)[O-]", "ligand_mw": "35.45%%103.12%%22.99%%132.16%%291.09%%96.06", "alternative_name": "", "ligand_name": "CHLORIDE ION%%N-methyl-L-alanine%%SODIUM ION%%L-ornithine%%IODO-PHENYLALANINE%%SULFATE ION", "pdb_classification": "IMMUNE SYSTEM", "global_stoichiometry": "Homo 6-mer - A6", "inchi_key": "VEXZGXHMUGYJMC-UHFFFAOYSA-M%%GDFAOVXKHJXLEI-VKHMYHEASA-N%%FKNQFGJONOIPTF-UHFFFAOYSA-N%%AHLPHDHHMVZTML-BYPYZUCNSA-N%%PZNQZSRPDOEBMS-QMMMGPOBSA-N%%QAOWNCQODCNURD-UHFFFAOYSA-L", "ligand_id": "CL%%MAA%%nan%%ORN%%PHI%%SO4"}