SMTL ID : 2ow0.3 (4 other biounits)

MMP-9 active site mutant with iodine-labeled carboxylate inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.117, H.121, H.127 Ligands: 6MR.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.117, A:H.121, A:H.127, 6MR.11 ZN.2: 4 residues within 4Å: Chain A: H.66, D.68, H.81, H.94 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.66, A:D.68, A:H.81, A:H.94 ZN.12: 4 residues within 4Å: Chain B: H.117, H.121, H.127 Ligands: 6MR.20 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.117, B:H.121, B:H.127 ZN.13: 4 residues within 4Å: Chain B: H.66, D.68, H.81, H.94 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.66, B:D.68, B:H.81, B:H.94 ZN.21: 4 residues within 4Å: Chain C: H.117, H.121, H.127 Ligands: 6MR.31 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.117, C:H.121, C:H.127 ZN.22: 4 residues within 4Å: Chain C: H.66, D.68, H.81, H.94 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.66, C:D.68, C:H.81, C:H.94 ZN.32: 4 residues within 4Å: Chain D: H.117, H.121, H.127 Ligands: 6MR.40 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.117, D:H.121, D:H.127, 6MR.40 ZN.33: 4 residues within 4Å: Chain D: H.66, D.68, H.81, H.94 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.66, D:D.68, D:H.81, D:H.94

16 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 6 residues within 4Å: Chain A: D.73, G.74, D.76, L.78, D.96, E.99 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.73, A:G.74, A:D.76, A:L.78, A:D.96 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: 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.2, H2O.2 CA.14: 4 residues within 4Å: Chain B: D.56, G.88, Q.90, D.92 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.56, B:G.88, B:Q.90, B:D.92, H2O.5, H2O.6 CA.15: 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.16: 4 residues within 4Å: Chain B: 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: 2 residues within 4Å: Chain B: S.40, T.43 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.40, B:T.43, H2O.6, H2O.7, H2O.7, H2O.9 CA.23: 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.11, H2O.12 CA.24: 6 residues within 4Å: Chain C: D.73, G.74, D.76, L.78, D.96, E.99 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.73, C:G.74, C:D.76, C:L.78, C:D.96 CA.25: 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.26: 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.10, H2O.10, H2O.11 CA.34: 4 residues within 4Å: Chain D: D.56, G.88, Q.90, D.92 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.56, D:G.88, D:Q.90, D:D.92, H2O.13, H2O.15 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.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.37: 2 residues within 4Å: Chain D: S.40, T.43 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:S.40, D:T.43, H2O.14, H2O.15, H2O.15, H2O.17

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

CL.7: 4 residues within 4Å: Chain A: G.104, S.110, F.112, F.141 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: R.34, F.112 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: L.38, P.145, P.146, L.147 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: N.18, Y.19 Chain B: N.18, Y.19 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.104, S.110, F.112, F.141 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: R.34, F.112 Chain C: K.105 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain C: G.104, S.110, F.112, F.141 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain C: R.34, F.112 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: L.38, P.145, P.146, L.147 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain C: N.18, Y.19 Chain D: N.18, Y.19 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain D: G.104, S.110, F.112, F.141 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain A: K.105 Chain D: R.34, F.112 Ligand excluded by PLIP

4 x 6MR: N-[(4'-IODOBIPHENYL-4-YL)SULFONYL]-D-TRYPTOPHAN(Non-covalent)

6MR.11: 17 residues within 4Å: Chain A: E.2, G.77, L.78, L.79, A.80, H.81, L.113, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.81, A:H.117, A:Y.139, A:Y.139 Hydrogen bonds: A:L.79, A:A.80, A:Q.118 Salt bridges: A:H.117, A:H.121, A:H.127 pi-Stacking: A:H.117 pi-Cation interactions: A:H.127 6MR.20: 14 residues within 4Å: Chain B: L.78, L.79, A.80, L.113, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:H.117, B:Y.139, B:Y.139 Hydrogen bonds: B:L.79, B:A.80, B:Q.118 Salt bridges: B:H.117, B:H.121, B:H.127 pi-Stacking: B:H.127 6MR.31: 17 residues within 4Å: Chain C: E.2, G.77, L.78, L.79, A.80, H.81, L.113, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.21 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:H.81, C:H.117, C:Y.139, C:Y.139 Hydrogen bonds: C:L.79, C:A.80, C:Q.118 Water bridges: C:H.127 Salt bridges: C:H.117, C:H.121, C:H.127 pi-Stacking: C:H.117 pi-Cation interactions: C:H.127 6MR.40: 14 residues within 4Å: Chain D: L.78, L.79, A.80, L.113, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.32 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:H.117, D:Y.139, D:Y.139 Hydrogen bonds: D:L.79, D:A.80, D:Q.118 Salt bridges: D:H.117, D:H.121, D:H.127 pi-Stacking: D:H.127

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 (MMP-9) (92 kDa type IV collagenase) (92 kDa gelatinase) (Gelatinase B) (GELB): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Matrix metalloproteinase-9 (MMP-9) (92 kDa type IV collagenase) (92 kDa gelatinase) (Gelatinase B) (GELB)

Related Entries With Identical Sequence