- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.44 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 5 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
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.1, H2O.3
CA.5: 4 residues within 4Å:- Chain A: D.188, D.232, S.280, D.329
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.188, A:D.232, A:S.280, A:D.329, H2O.1
CA.6: 6 residues within 4Å:- Chain A: I.190, A.234, A.282, V.331
- Ligands: CL.8, CL.9
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:I.190, A:A.234, A:A.282, A:V.331
CA.7: 3 residues within 4Å:- Chain A: D.25, D.100, E.102
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.10: 9 residues within 4Å:- Chain A: K.37, N.112, Y.143, G.145, K.146, S.147, H.148, F.149
- Ligands: PGO.20
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:K.37, A:K.37, A:N.112, A:Y.143, A:Y.143, A:G.145, A:H.148, A:F.149
GOL.11: 1 residues within 4Å:- Chain A: I.259
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:I.259
GOL.12: 7 residues within 4Å:- Chain A: S.186, L.187, D.188, K.201, K.327, D.329, G.343
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.186, A:D.188, A:K.201, A:K.327
- 16 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
PGO.13: 6 residues within 4Å:- Chain A: T.144, S.147, F.149, M.150, P.175, R.203
Ligand excluded by PLIPPGO.14: 9 residues within 4Å:- Chain A: P.133, G.134, A.135, F.138, I.140, Y.141, T.142, L.219
- Chain B: Y.16
Ligand excluded by PLIPPGO.15: 2 residues within 4Å:- Chain A: G.166, D.167
Ligand excluded by PLIPPGO.16: 3 residues within 4Å:- Chain A: G.336, W.352
- Ligands: PGO.17
Ligand excluded by PLIPPGO.17: 4 residues within 4Å:- Chain A: N.335, Y.337, W.352
- Ligands: PGO.16
Ligand excluded by PLIPPGO.18: 5 residues within 4Å:- Chain A: E.286, D.287, T.288, G.289, T.305
Ligand excluded by PLIPPGO.19: 7 residues within 4Å:- Chain A: P.178, D.179, D.182, S.184, L.185, K.201
- Ligands: PEG.31
Ligand excluded by PLIPPGO.20: 5 residues within 4Å:- Chain A: K.33, A.34, S.106, N.112
- Ligands: GOL.10
Ligand excluded by PLIPPGO.21: 2 residues within 4Å:- Chain A: T.105, S.107
Ligand excluded by PLIPPGO.22: 4 residues within 4Å:- Chain A: P.273, Q.298, W.300, P.314
Ligand excluded by PLIPPGO.23: 3 residues within 4Å:- Chain A: Q.298, P.314, L.316
Ligand excluded by PLIPPGO.24: 6 residues within 4Å:- Chain A: S.192, E.236, P.238, H.284, E.286, E.333
Ligand excluded by PLIPPGO.25: 6 residues within 4Å:- Chain A: Y.337, S.350, W.352, S.353, R.355, V.357
Ligand excluded by PLIPPGO.26: 3 residues within 4Å:- Chain A: Y.313, R.315, D.320
Ligand excluded by PLIPPGO.27: 3 residues within 4Å:- Chain A: G.262, Y.263, P.264
Ligand excluded by PLIPPGO.33: 4 residues within 4Å:- Chain A: L.8
- Chain B: A.9, R.11, Y.12
Ligand excluded by PLIP- 5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.28: 6 residues within 4Å:- Chain A: T.197, L.208, P.210, S.364, I.365, W.367
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:L.208
- Water bridges: A:T.197, A:K.334
PEG.29: 7 residues within 4Å:- Chain A: G.145, K.146, K.221, P.228, N.229, R.230, R.247
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:K.146, A:K.221, A:N.229, A:R.230, A:R.247, A:R.247
PEG.30: 3 residues within 4Å:- Chain A: T.177, P.178, D.179
No protein-ligand interaction detected (PLIP)PEG.31: 7 residues within 4Å:- Chain A: S.184, L.185, S.186, K.201, G.343, P.344
- Ligands: PGO.19
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.186, A:K.201
PEG.32: 3 residues within 4Å:- Chain A: H.209, P.210, Q.211
No protein-ligand interaction detected (PLIP)- 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
AB
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.44 Å
- Oligo State
- hetero-1-1-mer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 5 x CA: CALCIUM ION(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 16 x PGO: S-1,2-PROPANEDIOL(Non-covalent)
- 5 x PEG: DI(HYDROXYETHYL)ETHER(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
AB
C