SMTL ID : 3dpe.1

Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.58, G.90, I.91, G.92, D.94 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.58, A:G.90, A:G.92, A:D.94, H2O.7 CA.2: 6 residues within 4Å: Chain A: D.75, G.76, N.78, I.80, D.98, E.101 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.75, A:G.76, A:N.78, A:I.80, A:D.98

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.68, D.70, H.83, H.96 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.68, A:D.70, A:H.83 ZN.4: 3 residues within 4Å: Chain A: H.118, H.122, H.128 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.118, A:H.122, A:H.128

1 x AXB: N-{[2-(2-amino-3,4-dioxocyclobut-1-en-1-yl)-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-4-oxo-3,5,6,8-tetrahydro-4H-thiopyrano[4',3':4,5]thieno[2,3-d]pyrimidine-2-carboxamide 7,7-dioxide(Non-covalent)

AXB.5: 20 residues within 4Å: Chain A: I.80, L.81, A.82, L.114, H.118, E.119, A.134, L.135, Y.137, P.138, N.139, Y.140, A.141, F.142, R.143, T.145, N.147, Y.148, S.149, P.151 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.118, A:Y.140, A:Y.140 Hydrogen bonds: A:A.82, A:A.134, A:P.138, A:A.141, A:A.141, A:R.143, A:R.143 pi-Stacking: A:H.118 pi-Cation interactions: A:R.143, A:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pochetti, G. et al., Extra Binding Region Induced by Non-Zinc Chelating Inhibitors into the S(1)' Subsite of Matrix Metalloproteinase 8 (MMP-8). J.Med.Chem. (2009)

Release Date

2009-03-03

Peptides

Neutrophil collagenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neutrophil collagenase

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