SMTL ID : 4fu4.2 (1 other biounit)

Human collagenase 3 (MMP-13) with peptide from pro-domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.119, H.123, H.129 Chain B: S.21, Y.22 Ligands: CL.21 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.69, A:D.71, A:D.71, A:H.84, A:H.97

4 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95 CA.5: 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.232, A:S.280, A:D.329, H2O.2, H2O.3 CA.6: 7 residues within 4Å: Chain A: I.190, T.191, A.234, Y.235, A.282, V.331 Ligands: CL.7 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.2

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 8 residues within 4Å: Chain A: A.189, I.190, A.234, A.281, A.282, A.330, V.331 Ligands: CA.6 Ligand excluded by PLIP CL.21: 8 residues within 4Å: Chain A: A.83, H.84, H.119, H.123 Chain B: R.20, S.21, Y.22 Ligands: ZN.1 Ligand excluded by PLIP

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: L.193, R.194, F.223, W.224, G.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.256 Water bridges: A:R.194 EDO.9: 5 residues within 4Å: Chain A: D.25, D.100, D.101, E.102, T.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.100 EDO.10: 4 residues within 4Å: Chain A: T.144, F.149, M.150, P.152 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.134, A:R.203 EDO.11: 2 residues within 4Å: Chain A: N.342, I.345 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: D.132, P.133, T.177, P.178, D.179 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: F.285, T.288, K.290, I.351 No protein-ligand interaction detected (PLIP) EDO.14: 1 residues within 4Å: Chain A: Y.1 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: Q.157, Q.160, S.161 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain A: Q.160, S.161, G.164 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.161 EDO.17: 6 residues within 4Å: Chain A: K.37, G.145, K.146, S.147, H.148, F.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.146, A:K.146, A:S.147, A:F.149 EDO.18: 6 residues within 4Å: Chain A: Y.332, K.334, Y.339, Q.346, S.364 Ligands: EDO.19 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.332, A:K.334, A:Y.339, A:S.364 EDO.19: 3 residues within 4Å: Chain A: S.364, W.367 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) EDO.20: 7 residues within 4Å: Chain A: S.43, T.46, P.47, L.48, N.49, G.166, D.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.48, A:G.166 EDO.22: 4 residues within 4Å: Chain A: H.129 Chain B: R.20, S.21, Y.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.21, B:S.21

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
B

B
D

Collagenase 3

Collagenase 3, pro-domain peptide

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