SMTL ID : 2jih.1 (1 other biounit)

Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine- Rich Domain (complex-form)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x 097: (2S,3R)-N~4~-[(1S)-2,2-dimethyl-1-(methylcarbamoyl)propyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide(Non-covalent)

097.1: 14 residues within 4Å: Chain A: D.116, T.117, L.118, G.119, T.146, H.149, E.150, H.153, H.159, A.179, S.180, M.181, L.182 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.116, A:M.181 Hydrogen bonds: A:L.118, A:E.150, A:S.180, A:L.182 Water bridges: A:A.121, A:A.121

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.149, H.153, H.159 Ligands: 097.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.149, A:H.153, A:H.159

4 x CD: CADMIUM ION(Non-covalent)

CD.3: 4 residues within 4Å: Chain A: E.9, D.92, D.213 Ligands: CD.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.92, A:D.92, A:D.213, H2O.2, H2O.4 CD.4: 3 residues within 4Å: Chain A: E.63, E.68 Ligands: NI.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.63, A:E.68, H2O.1, H2O.1 CD.6: 1 residues within 4Å: Chain A: H.28 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.28, H2O.2 CD.7: 6 residues within 4Å: Chain A: E.9, D.92, D.99, C.210, D.213 Ligands: CD.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.9, A:D.92, A:D.99, A:C.210, A:D.213

7 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 1 residues within 4Å: Chain A: E.242 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.242, A:E.242 NI.8: 2 residues within 4Å: Chain A: E.68 Ligands: CD.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.68, A:E.68, H2O.1, H2O.1 NI.10: 1 residues within 4Å: Chain A: H.176 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.176, H2O.3 NI.11: 2 residues within 4Å: Chain A: E.242, D.243 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.243 NI.12: 1 residues within 4Å: Chain A: H.246 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.246, H2O.4 NI.13: 1 residues within 4Å: Chain A: H.273 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.273, H2O.3, H2O.4 NI.17: 1 residues within 4Å: Chain A: H.187 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.187, H2O.3

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 1 residues within 4Å: Chain A: H.87 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: V.266, L.267 No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.14: 7 residues within 4Å: Chain A: D.108, L.109, C.115, D.116, T.117, E.137 Ligands: NA.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.109, A:D.116 NA.15: 3 residues within 4Å: Chain A: D.108, C.115 Ligands: NA.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.108 NA.16: 7 residues within 4Å: Chain A: P.158, D.160, C.165, M.178, S.192, C.194, S.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.192, A:S.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gerhardt, S. et al., Crystal structures of human ADAMTS-1 reveal a conserved catalytic domain and a disintegrin-like domain with a fold homologous to cysteine-rich domains. J. Mol. Biol. (2007)

Release Date

2008-01-15

Peptides

ADAMTS-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ADAMTS-1

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