- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.74 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x ZN: ZINC ION(Non-covalent)
- 14 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
CA.11: 6 residues within 4Å:- Chain B: D.79, G.80, S.82, L.84, D.102, E.105
6 PLIP interactions:6 interactions with chain B- Metal complexes: B:D.79, B:G.80, B:S.82, B:L.84, B:D.102, B:E.105
CA.12: 6 residues within 4Å:- Chain B: A.61, D.62, N.94, Y.95, G.96, D.98
6 PLIP interactions:4 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.62, B:N.94, B:G.96, B:D.98, H2O.9, H2O.10
CA.13: 3 residues within 4Å:- Chain B: D.28, D.103, E.105
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.28, B:D.103, B:E.105, H2O.10, H2O.11
CA.14: 1 residues within 4Å:- Chain B: H.151
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:H.151, H2O.16, H2O.16
CA.19: 7 residues within 4Å:- Chain C: D.79, G.80, P.81, S.82, L.84, D.102, E.105
6 PLIP interactions:6 interactions with chain C- Metal complexes: C:D.79, C:G.80, C:S.82, C:L.84, C:D.102, C:E.105
CA.20: 5 residues within 4Å:- Chain C: D.62, N.94, Y.95, G.96, D.98
6 PLIP interactions:4 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.62, C:N.94, C:G.96, C:D.98, H2O.17, H2O.18
CA.21: 4 residues within 4Å:- Chain C: T.26, D.28, D.103, E.105
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.28, C:D.28, C:D.103, C:D.103, C:E.105
CA.27: 6 residues within 4Å:- Chain D: D.79, G.80, S.82, L.84, D.102, E.105
6 PLIP interactions:6 interactions with chain D- Metal complexes: D:D.79, D:G.80, D:S.82, D:L.84, D:D.102, D:E.105
CA.28: 6 residues within 4Å:- Chain D: A.61, D.62, N.94, Y.95, G.96, D.98
6 PLIP interactions:4 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.62, D:N.94, D:G.96, D:D.98, H2O.25, H2O.26
CA.29: 3 residues within 4Å:- Chain D: D.28, D.103, E.105
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.28, D:D.103, D:E.105, H2O.26, H2O.27
CA.30: 1 residues within 4Å:- Chain D: H.151
3 PLIP interactions:1 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:H.151, H2O.32, H2O.32
- 2 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
SO4.22: 3 residues within 4Å:- Chain C: E.35, K.39, R.55
13 PLIP interactions:13 interactions with chain C- Hydrogen bonds: C:Y.20
- Water bridges: C:E.35, C:E.35, C:E.35, C:K.39, C:K.39, C:K.39, C:R.55, C:R.55, C:R.55, C:R.55
- Salt bridges: C:K.39, C:R.55
- 4 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
SP6.15: 19 residues within 4Å:- Chain B: F.117, 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
- Ligands: HAE.16
13 PLIP interactions:13 interactions with chain B- Hydrophobic interactions: B:F.117, B:H.122, B:L.139, B:Y.144, B:F.152, B:F.152
- Hydrogen bonds: B:T.145, B:T.147, B:M.153
- Water bridges: B:T.147, B:T.147
- pi-Stacking: B:H.122, B:Y.144
SP6.23: 17 residues within 4Å:- Chain C: 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
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:H.122, C:L.139, C:Y.144, C:F.152, C:F.152, C:F.152
- Hydrogen bonds: C:T.145, C:T.147, C:K.149, C:M.153
- pi-Stacking: C:H.122, C:Y.146
SP6.31: 19 residues within 4Å:- Chain D: F.117, 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
- Ligands: HAE.32
11 PLIP interactions:11 interactions with chain D- Hydrophobic interactions: D:F.117, D:H.122, D:L.139, D:Y.144, D:F.152, D:F.152
- Hydrogen bonds: D:T.145, D:T.147, D:M.153
- pi-Stacking: D:H.122, D:Y.144
- 4 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
HAE.16: 8 residues within 4Å:- Chain B: A.86, H.122, E.123, H.126, H.132, P.142
- Ligands: ZN.9, SP6.15
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.123, B:H.132
- Water bridges: B:A.86
HAE.24: 8 residues within 4Å:- Chain C: L.84, A.86, H.87, H.122, E.123, H.126, H.132
- Ligands: ZN.17
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.84, C:H.87
- Hydrogen bonds: C:A.86
- Water bridges: C:A.86, C:E.123, C:E.123
HAE.32: 8 residues within 4Å:- Chain D: A.86, H.122, E.123, H.126, H.132, P.142
- Ligands: ZN.25, SP6.31
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:E.123, D:H.132
- Water bridges: D: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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.74 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x ZN: ZINC ION(Non-covalent)
- 14 x CA: CALCIUM ION(Non-covalent)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 4 x SP6: BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE(Non-covalent)
- 4 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B