SMTL ID : 4h82.2 (1 other biounit)

Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.117, H.121, H.127 Ligands: L29.16 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.117, A:H.121, A:H.127 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.15: 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.17: 4 residues within 4Å: Chain B: H.117, H.121, H.127 Ligands: L29.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.117, B:H.121, B:H.127

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.56, G.88, Q.90, D.92 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:Q.90, A:D.92, H2O.1, H2O.2 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: 6 residues within 4Å: Chain A: S.20, D.22, D.97, E.99, L.100, 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.18: 7 residues within 4Å: Chain B: D.73, G.74, D.76, G.77, L.78, D.96, E.99 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.73, B:G.74, B:L.78, B:D.96, B:E.99 CA.19: 3 residues within 4Å: Chain B: D.22, D.97, E.99 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.22, B:D.97, B:E.99 CA.20: 4 residues within 4Å: Chain B: D.56, G.88, Q.90, D.92 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.56, B:G.88, B:Q.90, H2O.7, H2O.7

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain A: D.68, G.69, Y.70 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.70, A:Y.70 PEG.9: 3 residues within 4Å: Chain A: S.129, V.130, P.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.129 PEG.10: 2 residues within 4Å: Chain A: K.105 Ligands: GOL.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.105, A:K.105 PEG.11: 1 residues within 4Å: Chain A: F.61 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.18, A:V.63 PEG.13: 4 residues within 4Å: Chain A: H.127, S.128, S.129, D.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.129, A:D.150 PEG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PPI: PROPANOIC ACID(Non-functional Binders)

PPI.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain A: K.105, F.141 Ligands: PEG.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.105, A:K.105 Water bridges: A:K.105, A:G.106, A:F.141

3 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.14: 5 residues within 4Å: Chain A: D.76, G.77 Chain B: Y.139, R.140 Ligands: PGO.23 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:D.76 Water bridges: A:D.73 Hydrogen bonds: B:R.140 PGO.21: 3 residues within 4Å: Chain B: F.112, P.145, P.146 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.112 PGO.23: 4 residues within 4Å: Chain B: G.106, G.108, Y.139 Ligands: PGO.14 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.108, B:F.141

1 x L29: N,N'-bis(2-{(biphenyl-4-ylsulfonyl)[(2R)-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]amino}ethyl)benzene-1,3-dicarboxamide (non-preferred name)(Non-covalent)

L29.16: 33 residues within 4Å: Chain A: G.77, L.78, L.79, A.80, H.81, L.113, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Chain B: G.77, L.78, L.79, A.80, L.113, V.114, H.117, Q.118, H.121, H.127, L.134, Y.136, P.137, M.138, Y.139 Ligands: ZN.1, ZN.17 28 PLIP interactions: 13 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:L.78, A:H.81, A:V.114, A:H.117, A:Y.139, B:L.78, B:L.79, B:L.113, B:V.114, B:V.114, B:H.117, B:L.134, B:P.137, B:Y.139 Hydrogen bonds: A:L.79, A:A.80, A:A.80, A:Q.118, A:H.127, B:A.80, B:A.80, B:Q.118, B:P.137, B:P.137 Water bridges: A:A.82, A:A.82 pi-Stacking: A:H.117, B:H.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antoni, C. et al., Crystallization of bi-functional ligand protein complexes. J.Struct.Biol. (2013)

Release Date

2013-05-01

Peptides

Matrix metalloproteinase-9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Matrix metalloproteinase-9

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