- 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: 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.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.2, H2O.5
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: 5 residues within 4Å:- Chain A: I.190, A.234, A.282, V.331
- Ligands: CL.8
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:I.190, A:A.234, A:A.282, A:V.331, H2O.1
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
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 7 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 9 residues within 4Å:- Chain A: M.26, E.30, K.33, A.34, K.37, S.106, N.112, F.114
- Ligands: GOL.13
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:K.33, A:A.34, A:K.37, A:K.37, A:S.106, A:S.106, A:N.112
- Water bridges: A:F.114
GOL.10: 4 residues within 4Å:- Chain A: H.240, D.241, L.242, N.255
No protein-ligand interaction detected (PLIP)GOL.11: 3 residues within 4Å:- Chain A: N.342, P.344, I.345
No protein-ligand interaction detected (PLIP)GOL.12: 5 residues within 4Å:- Chain A: E.318, P.322, G.323, I.324, G.325
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:G.323, A:G.325
- Water bridges: A:F.321, A:I.324
GOL.13: 10 residues within 4Å:- Chain A: K.37, N.112, F.114, Y.143, G.145, K.146, S.147, H.148, F.149
- Ligands: GOL.9
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.37, A:N.112, A:T.144, A:S.147, A:F.149
GOL.14: 6 residues within 4Å:- Chain A: E.275, V.276, K.277, S.295, G.296
- Ligands: PGO.18
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.277
GOL.15: 3 residues within 4Å:- Chain A: T.197, P.210, K.334
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:T.197, A:Y.332, A:Y.332, A:K.334
- Water bridges: A:H.209, A:W.367
- 12 x PGO: S-1,2-PROPANEDIOL(Non-covalent)(Non-functional Binders)
PGO.16: 4 residues within 4Å:- Chain A: K.131, D.132, P.133, L.217
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.217
- Hydrogen bonds: A:K.131
- Water bridges: A:D.132, A:D.132
PGO.17: 5 residues within 4Å:- Chain A: M.61, S.63, Y.92, D.95, H.97
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:M.61, A:S.63, A:H.97
PGO.18: 4 residues within 4Å:- Chain A: P.273, E.275, Q.298
- Ligands: GOL.14
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:P.273, A:E.275
- Hydrogen bonds: A:Q.298, A:Q.298
PGO.19: 4 residues within 4Å:- Chain A: S.43, T.46, P.47, L.48
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.48
- Water bridges: A:P.47
PGO.20: 6 residues within 4Å:- Chain A: N.2, H.129, S.130, K.131, P.139
- Ligands: PEG.31
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:K.131
PGO.21: 6 residues within 4Å:- Chain A: T.7, K.9, W.10, S.11, P.88, G.89
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.11, A:S.11
PGO.22: 5 residues within 4Å:- Chain A: Y.332, K.334, Q.346, M.360, I.365
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.334, A:Q.346
PGO.23: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)PGO.24: 5 residues within 4Å:- Chain A: F.149, M.150, P.152, P.175, R.203
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:P.175
- Hydrogen bonds: A:M.150
PGO.25: 5 residues within 4Å:- Chain A: H.237, S.239, H.284, E.286, D.304
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.237, A:D.304
PGO.26: 3 residues within 4Å:- Chain A: R.194, D.241, N.255
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.194, A:R.194
PGO.27: 3 residues within 4Å:- Chain A: D.179, D.182, P.183
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:D.179
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.28: 6 residues within 4Å:- Chain A: S.108, Y.141, T.142, Y.143, K.221
- Chain B: H.18
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.143
PEG.29: 2 residues within 4Å:- Chain A: Y.1, V.3
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:V.3
- Water bridges: A:N.2, A:V.3
PEG.30: 9 residues within 4Å:- Chain A: P.133, A.135, F.138, I.140, T.142, F.218, L.219, S.222
- Chain B: Y.16
7 PLIP interactions:6 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:T.142, A:T.142, A:L.219, A:S.222, A:S.222, B:Y.16
- Water bridges: A:T.142
PEG.31: 7 residues within 4Å:- Chain A: H.129, P.139
- Chain B: L.13, R.14, S.15, Y.17
- Ligands: PGO.20
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.13, B:S.15
- Water bridges: B:R.14
- 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
BB
D
- 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)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 12 x PGO: S-1,2-PROPANEDIOL(Non-covalent)(Non-functional Binders)
- 4 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
BB
D