- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x ZN: ZINC ION(Non-covalent)
- 20 x CA: CALCIUM ION(Non-covalent)
CA.3: 7 residues within 4Å:- Chain A: D.73, G.74, K.75, D.76, L.78, D.96, E.99
6 PLIP interactions:6 interactions with chain A- Metal complexes: A:D.73, A:G.74, A:D.76, A:L.78, A:D.96, A:E.99
CA.4: 4 residues within 4Å:- Chain A: D.56, G.88, Q.90, D.92
6 PLIP interactions:4 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.56, A:G.88, A:Q.90, A:D.92, H2O.3, H2O.4
CA.5: 5 residues within 4Å:- Chain A: S.20, D.22, D.97, E.99, W.101
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.22, A:D.97, A:D.97, A:E.99
CA.6: 6 residues within 4Å:- Chain A: S.102, L.103, G.104, G.106, Q.107, G.108
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:Q.107, H2O.1, H2O.4
CA.7: 2 residues within 4Å:- Chain A: S.40, T.43
5 PLIP interactions:2 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:S.40, A:T.43, H2O.2, H2O.3, H2O.3
CA.14: 6 residues within 4Å:- Chain B: D.73, G.74, D.76, L.78, D.96, E.99
6 PLIP interactions:6 interactions with chain B- Metal complexes: B:D.73, B:G.74, B:D.76, B:L.78, B:D.96, B:E.99
CA.15: 4 residues within 4Å:- Chain B: D.56, G.88, Q.90, D.92
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.56, B:G.88, B:Q.90, B:D.92
CA.16: 5 residues within 4Å:- Chain B: S.20, D.22, D.97, E.99, W.101
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.22, B:D.97, B:D.97, B:E.99
CA.17: 7 residues within 4Å:- Chain B: S.102, L.103, G.104, K.105, G.106, Q.107
- Chain C: L.103
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:S.102, B:L.103, B:K.105, H2O.6, H2O.7
CA.18: 2 residues within 4Å:- Chain B: S.40, T.43
4 PLIP interactions:2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:S.40, B:T.43, H2O.5, H2O.7
CA.24: 7 residues within 4Å:- Chain C: D.73, G.74, K.75, D.76, L.78, D.96, E.99
6 PLIP interactions:6 interactions with chain C- Metal complexes: C:D.73, C:G.74, C:D.76, C:L.78, C:D.96, C:E.99
CA.25: 4 residues within 4Å:- Chain C: D.56, G.88, Q.90, D.92
6 PLIP interactions:4 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.56, C:G.88, C:Q.90, C:D.92, H2O.10, H2O.11
CA.26: 5 residues within 4Å:- Chain C: S.20, D.22, D.97, E.99, W.101
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.22, C:D.97, C:D.97, C:E.99
CA.27: 6 residues within 4Å:- Chain C: S.102, L.103, G.104, G.106, Q.107, G.108
3 PLIP interactions:1 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:Q.107, H2O.8, H2O.11
CA.28: 2 residues within 4Å:- Chain C: S.40, T.43
5 PLIP interactions:2 interactions with chain C, 3 Ligand-Water interactions- Metal complexes: C:S.40, C:T.43, H2O.9, H2O.10, H2O.11
CA.35: 6 residues within 4Å:- Chain D: D.73, G.74, D.76, L.78, D.96, E.99
6 PLIP interactions:6 interactions with chain D- Metal complexes: D:D.73, D:G.74, D:D.76, D:L.78, D:D.96, D:E.99
CA.36: 4 residues within 4Å:- Chain D: D.56, G.88, Q.90, D.92
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.56, D:G.88, D:Q.90, D:D.92
CA.37: 5 residues within 4Å:- Chain D: S.20, D.22, D.97, E.99, W.101
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.22, D:D.97, D:D.97, D:E.99
CA.38: 7 residues within 4Å:- Chain A: L.103
- Chain D: S.102, L.103, G.104, K.105, G.106, Q.107
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:S.102, D:L.103, D:K.105, H2O.13, H2O.14
CA.39: 2 residues within 4Å:- Chain D: S.40, T.43
4 PLIP interactions:2 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:S.40, D:T.43, H2O.13, H2O.14
- 10 x CL: CHLORIDE ION(Non-functional Binders)
CL.8: 4 residues within 4Å:- Chain A: G.104, S.110, F.112, F.141
Ligand excluded by PLIPCL.9: 2 residues within 4Å:- Chain A: R.34, F.112
Ligand excluded by PLIPCL.10: 4 residues within 4Å:- Chain A: N.18, Y.19
- Chain B: N.18, Y.19
Ligand excluded by PLIPCL.19: 5 residues within 4Å:- Chain B: L.103, G.104, S.110, F.112, F.141
Ligand excluded by PLIPCL.20: 3 residues within 4Å:- Chain B: R.34, F.112
- Chain C: K.105
Ligand excluded by PLIPCL.29: 4 residues within 4Å:- Chain C: G.104, S.110, F.112, F.141
Ligand excluded by PLIPCL.30: 2 residues within 4Å:- Chain C: R.34, F.112
Ligand excluded by PLIPCL.31: 4 residues within 4Å:- Chain C: N.18, Y.19
- Chain D: N.18, Y.19
Ligand excluded by PLIPCL.40: 5 residues within 4Å:- Chain D: L.103, G.104, S.110, F.112, F.141
Ligand excluded by PLIPCL.41: 3 residues within 4Å:- Chain A: K.105
- Chain D: R.34, F.112
Ligand excluded by PLIP- 4 x 4MR: 5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN-2-YLPIPERAZIN-1-YL)PYRIMIDINE-2,4,6(2H,3H)-TRIONE(Non-covalent)
4MR.11: 17 residues within 4Å:- Chain A: G.77, L.78, L.79, A.80, H.81, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139, R.140
- Ligands: ZN.1
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:V.114, A:H.117, A:Y.139
- Hydrogen bonds: A:L.79, A:A.80, A:A.80, A:Q.118
- pi-Cation interactions: A:H.117
4MR.21: 16 residues within 4Å:- Chain B: L.78, L.79, A.80, L.113, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139, R.140
- Ligands: ZN.12
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:L.113, B:V.114, B:H.117, B:Y.139
- Hydrogen bonds: B:L.79, B:A.80, B:A.80, B:Q.118, B:H.127
- Water bridges: B:A.82
- pi-Stacking: B:H.117
4MR.32: 17 residues within 4Å:- Chain C: G.77, L.78, L.79, A.80, H.81, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139, R.140
- Ligands: ZN.22
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:V.114, C:H.117, C:Y.139
- Hydrogen bonds: C:L.79, C:A.80, C:A.80, C:Q.118, C:H.127
- pi-Cation interactions: C:H.117
4MR.42: 16 residues within 4Å:- Chain D: L.78, L.79, A.80, L.113, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139, R.140
- Ligands: ZN.33
10 PLIP interactions:10 interactions with chain D- Hydrophobic interactions: D:L.113, D:V.114, D:H.117, D:Y.139
- Hydrogen bonds: D:L.79, D:A.80, D:A.80, D:Q.118
- Water bridges: D:A.82
- pi-Stacking: D:H.117
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tochowicz, A. et al., Crystal Structures of MMP-9 Complexes with Five Inhibitors: Contribution of the Flexible Arg424 Side-chain to Selectivity. J.Mol.Biol. (2007)
- Release Date
- 2007-06-19
- Peptides
- Matrix metalloproteinase-9 (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gelatinase) (Gelatinase B) (GELB): ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-tetramer
- Ligands
- 8 x ZN: ZINC ION(Non-covalent)
- 20 x CA: CALCIUM ION(Non-covalent)
- 10 x CL: CHLORIDE ION(Non-functional Binders)
- 4 x 4MR: 5-(4-PHENOXYPHENYL)-5-(4-PYRIMIDIN-2-YLPIPERAZIN-1-YL)PYRIMIDINE-2,4,6(2H,3H)-TRIONE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Tochowicz, A. et al., Crystal Structures of MMP-9 Complexes with Five Inhibitors: Contribution of the Flexible Arg424 Side-chain to Selectivity. J.Mol.Biol. (2007)
- Release Date
- 2007-06-19
- Peptides
- Matrix metalloproteinase-9 (EC 3.4.24.35) (MMP-9) (92 kDa type IV collagenase) (92 kDa gelatinase) (Gelatinase B) (GELB): ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
AD
B