SMTL ID : 3ljt.1

Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x LA3: (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide(Non-covalent)

LA3.1: 18 residues within 4Å: Chain A: D.115, T.116, L.117, G.118, H.141, F.144, T.145, H.148, E.149, H.152, H.158, L.176, S.178, S.179, I.180, L.181, I.184 Ligands: ZN.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.115, A:F.144, A:T.145, A:I.180, A:L.181, A:L.181, A:I.184 Hydrogen bonds: A:L.117, A:G.118, A:S.179, A:L.181 pi-Stacking: A:H.148

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: G.123, T.124, S.127, H.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.123 Water bridges: A:C.126, A:G.205

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.148, H.152, H.158 Ligands: LA3.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.148, A:H.152, A:H.158

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.8, D.98, C.209, D.212 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.8, A:D.98, A:C.209, H2O.1, H2O.2 CA.5: 4 residues within 4Å: Chain A: E.8, D.212, L.213, P.214 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.8, A:D.212, H2O.3, H2O.4, H2O.6 CA.6: 5 residues within 4Å: Chain A: D.107, L.108, C.114, T.116, E.136 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.107, A:L.108, A:C.114, A:T.116, A:E.136, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shieh, H.S. et al., Structure analysis reveals the flexibility of the ADAMTS-5 active site. Protein Sci. (2011)

Release Date

2010-03-31

Peptides

A disintegrin and metalloproteinase with thrombospondin motifs 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

A disintegrin and metalloproteinase with thrombospondin motifs 5