SMTL ID : 2ow9.1 (2 other biounits)

Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.122, H.126, H.132 Ligands: HAE.8 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.122, A:H.126, A:H.132, H2O.6, HAE.8 ZN.2: 4 residues within 4Å: Chain A: H.72, D.74, H.87, H.100 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.72, A:D.74, A:H.87, A:H.100

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.79, G.80, P.81, S.82, L.84, D.102, E.105 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.79, A:G.80, A:S.82, A:L.84, A:D.102, A:E.105 CA.4: 5 residues within 4Å: Chain A: D.62, N.94, Y.95, G.96, D.98 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.62, A:N.94, A:G.96, A:D.98, H2O.1, H2O.1 CA.5: 4 residues within 4Å: Chain A: T.26, D.28, D.103, E.105 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.28, A:D.28, A:D.103, A:D.103, A:E.105

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain A: E.35, K.39, R.55 10 PLIP interactions: 10 interactions with chain A Water bridges: A:Y.20, A:E.35, A:K.39, A:K.39, A:K.39, A:R.55, A:R.55, A:R.55 Salt bridges: A:K.39, A:R.55

1 x SP6: BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE(Non-covalent)

SP6.7: 17 residues within 4Å: Chain A: L.118, V.119, H.122, A.138, L.139, F.141, P.142, I.143, Y.144, T.145, Y.146, T.147, K.149, S.150, H.151, F.152, M.153 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.122, A:L.139, A:Y.144, A:F.152, A:F.152, A:F.152 Hydrogen bonds: A:T.145, A:T.147, A:K.149, A:M.153 Water bridges: A:T.147 pi-Stacking: A:H.122, A:Y.146

1 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.8: 8 residues within 4Å: Chain A: L.84, A.86, H.87, H.122, E.123, H.126, H.132 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.84, A:H.87 Hydrogen bonds: A:A.86 Water bridges: A:A.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, A.R. et al., Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia side effects. J.Biol.Chem. (2007)

Release Date

2007-02-27

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Collagenase 3

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