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

Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.119, H.123, H.129 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.119, A:H.123, A:H.129, H2O.1, H2O.1 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.6: 3 residues within 4Å: Chain B: H.119, H.123, H.129 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.119, B:H.123, B:H.129, H2O.11, H2O.12 ZN.7: 4 residues within 4Å: Chain B: H.69, D.71, 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 ZN.11: 3 residues within 4Å: Chain C: H.119, H.123, H.129 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.119, C:H.123, C:H.129, H2O.20, H2O.21 ZN.12: 4 residues within 4Å: Chain C: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.69, C:D.71, C:H.84, C:H.97 ZN.16: 3 residues within 4Å: Chain D: H.119, H.123, H.129 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.119, D:H.123, D:H.129, H2O.31, H2O.31 ZN.17: 4 residues within 4Å: Chain D: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.69, D:D.71, D:H.84, D:H.97

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102 CA.4: 5 residues within 4Å: Chain A: D.59, N.91, Y.92, G.93, D.95 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:G.93, A:D.95, H2O.4, H2O.5 CA.8: 6 residues within 4Å: Chain B: D.76, G.77, S.79, L.81, D.99, E.102 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.76, B:G.77, B:S.79, B:L.81, B:D.99 CA.9: 6 residues within 4Å: Chain B: A.58, D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.59, B:N.91, B:G.93, B:D.95, H2O.14, H2O.16 CA.13: 6 residues within 4Å: Chain C: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.76, C:G.77, C:S.79, C:L.81, C:D.99, C:E.102 CA.14: 5 residues within 4Å: Chain C: D.59, N.91, Y.92, G.93, D.95 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.59, C:G.93, C:D.95, H2O.24, H2O.24 CA.18: 6 residues within 4Å: Chain D: D.76, G.77, S.79, L.81, D.99, E.102 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.76, D:G.77, D:S.79, D:L.81, D:D.99 CA.19: 6 residues within 4Å: Chain D: A.58, D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.59, D:N.91, D:G.93, D:D.95, H2O.33, H2O.36

4 x PB5: N,N'-BIS(PYRIDIN-3-YLMETHYL)PYRIMIDINE-4,6-DICARBOXAMIDE(Non-covalent)

PB5.5: 17 residues within 4Å: Chain A: N.112, F.114, L.115, V.116, H.119, A.135, L.136, F.138, I.140, Y.141, T.142, Y.143, T.144, K.146, S.147, H.148, F.149 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.114, A:L.115, A:H.119 Hydrogen bonds: A:A.135, A:T.142, A:T.144 Water bridges: A:T.144, A:H.148, A:F.149 pi-Stacking: A:H.119, A:Y.141 PB5.10: 18 residues within 4Å: Chain B: N.112, F.114, L.115, V.116, H.119, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, Y.143, T.144, K.146, S.147, H.148, F.149 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.114, B:L.115, B:H.119, B:Y.143 Hydrogen bonds: B:A.135, B:T.142, B:T.144 Water bridges: B:T.144, B:H.148, B:F.149 pi-Stacking: B:H.119 PB5.15: 17 residues within 4Å: Chain C: N.112, F.114, L.115, V.116, H.119, A.135, L.136, F.138, I.140, Y.141, T.142, Y.143, T.144, K.146, S.147, H.148, F.149 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.114, C:L.115, C:H.119 Hydrogen bonds: C:A.135, C:T.142, C:T.144 Water bridges: C:H.148, C:F.149 pi-Stacking: C:H.119, C:Y.141 PB5.20: 18 residues within 4Å: Chain D: N.112, F.114, L.115, V.116, H.119, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, Y.143, T.144, K.146, S.147, H.148, F.149 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.114, D:L.115, D:H.119, D:Y.143 Hydrogen bonds: D:A.135, D:T.142, D:T.144 Water bridges: D:H.148, D:F.149 pi-Stacking: D:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engel, C.K. et al., Structural basis for the highly selective inhibition of MMP-13. Chem.Biol. (2005)

Release Date

2005-10-26

Peptides

Collagenase 3: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Collagenase 3

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