SMTL ID : 1q3a.2 (2 other biounits)

Crystal structure of the catalytic domain of human matrix metalloproteinase 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: NGH.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97 ZN.7: 4 residues within 4Å: Chain B: H.119, H.123, H.129 Ligands: NGH.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.119, B:H.123, B:H.129, H2O.6 ZN.8: 5 residues within 4Å: Chain B: H.69, D.71, Y.73, H.84, H.97 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.69, B:D.71, B:H.84, B:H.97

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.76, G.77, G.79, S.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:G.79, A:S.81, A:D.99, A:E.102 CA.4: 6 residues within 4Å: Chain A: A.58, D.59, G.91, L.92, Y.93, D.95 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:G.91, A:Y.93, A:D.95, H2O.2 CA.5: 3 residues within 4Å: Chain A: D.25, D.100, E.102 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:D.100, A:E.102, H2O.1, H2O.1 CA.9: 7 residues within 4Å: Chain B: D.76, G.77, G.79, H.80, S.81, D.99, E.102 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.76, B:G.79, B:S.81, B:D.99, B:E.102 CA.10: 4 residues within 4Å: Chain B: D.59, G.91, Y.93, D.95 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.59, B:G.91, B:Y.93, B:D.95, H2O.6 CA.11: 5 residues within 4Å: Chain B: D.25, D.100, E.102, K.103, W.104 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.25, B:D.25, B:D.100, B:D.100, B:E.102

2 x NGH: N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID(Non-covalent)

NGH.6: 15 residues within 4Å: Chain A: S.81, L.82, A.83, L.115, V.116, H.119, E.120, H.123, H.129, L.136, P.139, L.140, Y.141 Chain B: H.80 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.116, A:Y.141 Hydrogen bonds: A:L.82, A:A.83, A:A.83 pi-Stacking: A:H.119 NGH.12: 16 residues within 4Å: Chain A: N.142, F.144 Chain B: H.80, S.81, L.82, A.83, V.116, H.119, E.120, H.123, H.129, L.136, P.139, L.140, Y.141 Ligands: ZN.7 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.82, B:V.116, B:Y.141, B:Y.141, A:F.144 Hydrogen bonds: B:L.82, B:A.83 Water bridges: B:H.119 Salt bridges: B:E.120 pi-Cation interactions: B:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertini, I. et al., Crystal structure of the catalytic domain of human matrix metalloproteinase 10. J.Mol.Biol. (2004)

Release Date

2004-04-06

Peptides

Stromelysin-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Stromelysin-2

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