- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.54 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 7 x CA: CALCIUM ION(Non-covalent)
CA.3: 3 residues within 4Å:- Chain A: D.25, D.100, E.102
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.25, A:D.25, A:D.100, A:D.100, A:E.102
CA.4: 7 residues within 4Å:- Chain A: D.76, G.77, P.78, 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.5: 5 residues within 4Å:- Chain A: D.59, N.91, Y.92, G.93, D.95
6 PLIP interactions:4 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.2, H2O.7
CA.6: 4 residues within 4Å:- Chain A: D.188, D.232, S.280, D.329
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.188, A:D.232, A:D.329, H2O.3, H2O.5
CA.7: 5 residues within 4Å:- Chain A: I.190, A.234, A.282, V.331
- Ligands: CL.8
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:I.190, A:A.234, A:A.282, A:V.331
CA.9: 3 residues within 4Å:- Chain A: S.43, T.46, G.166
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:S.43, A:T.46, H2O.3, H2O.3
CA.10: 4 residues within 4Å:- Chain A: F.138, I.140, Y.141, T.142
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:I.140, H2O.2
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 11 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
PGO.11: 5 residues within 4Å:- Chain A: M.150, P.175, R.203, R.230
- Ligands: PGO.19
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.230, A:R.230
- Water bridges: A:R.203, A:R.203
PGO.14: 7 residues within 4Å:- Chain A: T.197, L.208, H.209, P.210, Q.212, W.367
- Ligands: PGO.15
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.212
PGO.15: 4 residues within 4Å:- Chain A: S.364, I.365, W.367
- Ligands: PGO.14
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:I.365
PGO.16: 2 residues within 4Å:- Chain A: S.222, Y.257
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.257
- Water bridges: A:S.222
PGO.17: 3 residues within 4Å:- Chain A: N.91, Y.92, D.95
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.91
- Water bridges: A:D.95
PGO.18: 2 residues within 4Å:- Chain A: G.336, W.352
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:W.352
PGO.19: 7 residues within 4Å:- Chain A: T.144, H.148, F.149, M.150, R.203
- Ligands: PGO.11, PGO.20
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:M.150, A:R.203
- Water bridges: A:R.203
PGO.20: 10 residues within 4Å:- Chain A: G.134, A.135, L.136, T.142, T.144, F.149, P.152, R.203, L.219
- Ligands: PGO.19
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:T.144, A:F.149, A:P.152
- Hydrogen bonds: A:T.142, A:R.203
PGO.21: 4 residues within 4Å:- Chain A: P.178, D.179, D.182, L.185
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:D.182, A:L.185
- Hydrogen bonds: A:D.179
- Water bridges: A:K.201
PGO.23: 4 residues within 4Å:- Chain A: Q.160, S.161, L.162, G.164
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:L.162
PGO.24: 7 residues within 4Å:- Chain A: K.37, F.114, Y.143, T.144, G.145, K.146, S.147
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.37, A:S.147, A:F.149
- Water bridges: A:H.148
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.12: 4 residues within 4Å:- Chain A: Q.212, D.214, A.215, E.216
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Q.212, A:A.215
- Water bridges: A:Q.212
GOL.13: 3 residues within 4Å:- Chain A: E.68, H.69, G.70
No protein-ligand interaction detected (PLIP)GOL.22: 3 residues within 4Å:- Chain A: P.314, R.315, L.316
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:P.314
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stura, E.A. et al., Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain. Faseb J. (2013)
- Release Date
- 2013-08-21
- Peptides
- Collagenase 3: A
Collagenase 3, pro-domain peptide: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
Y
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.54 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 7 x CA: CALCIUM ION(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 11 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stura, E.A. et al., Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain. Faseb J. (2013)
- Release Date
- 2013-08-21
- Peptides
- Collagenase 3: A
Collagenase 3, pro-domain peptide: B - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
Y