SMTL ID : 5ue3.3 (2 other biounits)

proMMP-9desFnII

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.65, V.67, H.192, H.196, H.202 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:H.192, A:H.196, A:H.202 ZN.2: 4 residues within 4Å: Chain A: H.141, D.143, H.156, H.169 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.141, A:D.143, A:H.156, A:H.169 ZN.10: 5 residues within 4Å: Chain B: C.65, V.67, H.192, H.196, H.202 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.65, B:H.192, B:H.196, B:H.202 ZN.11: 4 residues within 4Å: Chain B: H.141, D.143, H.156, H.169 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.141, B:D.143, B:H.156, B:H.169 ZN.19: 5 residues within 4Å: Chain C: C.65, V.67, H.192, H.196, H.202 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.65, C:H.192, C:H.196, C:H.202 ZN.20: 4 residues within 4Å: Chain C: H.141, D.143, H.156, H.169 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.141, C:D.143, C:H.156, C:H.169 ZN.26: 5 residues within 4Å: Chain D: C.65, V.67, H.192, H.196, H.202 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.65, D:H.192, D:H.196, D:H.202 ZN.27: 4 residues within 4Å: Chain D: H.141, D.143, H.156, H.169 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.141, D:D.143, D:H.156, D:H.169

10 x CA: CALCIUM ION(Non-covalent)

CA.3: 7 residues within 4Å: Chain A: D.148, G.149, K.150, D.151, L.153, D.171, E.174 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.148, A:G.149, A:D.151, A:L.153, A:D.171, A:E.174 CA.4: 4 residues within 4Å: Chain A: D.131, G.163, Q.165, D.167 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:G.163, A:Q.165, A:D.167, H2O.2, H2O.3 CA.12: 7 residues within 4Å: Chain B: D.148, G.149, K.150, D.151, L.153, D.171, E.174 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.148, B:G.149, B:D.151, B:L.153, B:D.171, B:E.174 CA.13: 4 residues within 4Å: Chain B: D.131, G.163, Q.165, D.167 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.131, B:G.163, B:Q.165, B:D.167, H2O.12, H2O.13 CA.21: 7 residues within 4Å: Chain C: D.148, G.149, K.150, D.151, L.153, D.171, E.174 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.148, C:G.149, C:D.151, C:L.153, C:D.171, C:E.174 CA.22: 3 residues within 4Å: Chain C: S.95, E.96, D.172 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.172, H2O.25, H2O.32 CA.23: 5 residues within 4Å: Chain C: A.130, D.131, G.163, Q.165, D.167 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.131, C:G.163, C:Q.165, C:D.167, H2O.22, H2O.24 CA.28: 7 residues within 4Å: Chain D: D.148, G.149, K.150, D.151, L.153, D.171, E.174 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.148, D:G.149, D:D.151, D:L.153, D:D.171, D:E.174 CA.29: 3 residues within 4Å: Chain D: S.95, E.96, D.172 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.172, H2O.37, H2O.45 CA.30: 5 residues within 4Å: Chain D: A.130, D.131, G.163, Q.165, D.167 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.131, D:G.163, D:Q.165, D:D.167, H2O.34, H2O.37

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: K.81, W.82, H.83, H.84 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.83 Water bridges: A:K.81, A:H.83, A:G.161 Salt bridges: A:H.84 SO4.6: 5 residues within 4Å: Chain A: S.177, K.180, G.181, Q.182, G.183 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.177, A:G.179, A:G.181, A:Q.182, A:G.183, A:G.183 Water bridges: A:L.178, A:L.178, A:L.178, A:K.180 SO4.7: 5 residues within 4Å: Chain A: D.69, L.70, G.71, R.72, D.201 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.71, A:G.71 Water bridges: A:D.201, A:H.202 Salt bridges: A:R.72 SO4.8: 4 residues within 4Å: Chain A: E.207, R.215, T.217, H.223 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.217 Water bridges: A:T.217, A:H.223 Salt bridges: A:R.215, A:H.223 SO4.14: 4 residues within 4Å: Chain B: K.81, W.82, H.83, H.84 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.83 Water bridges: B:K.81, B:H.83, B:G.161 Salt bridges: B:H.84 SO4.15: 5 residues within 4Å: Chain B: S.177, K.180, G.181, Q.182, G.183 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.177, B:G.179, B:G.181, B:Q.182, B:G.183, B:G.183 Water bridges: B:L.178, B:L.178, B:L.178, B:K.180 SO4.16: 5 residues within 4Å: Chain B: D.69, L.70, G.71, R.72, D.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.71, B:G.71 Water bridges: B:H.202 Salt bridges: B:R.72 SO4.17: 4 residues within 4Å: Chain B: E.207, R.215, T.217, H.223 4 PLIP interactions: 4 interactions with chain B Water bridges: B:T.217, B:H.223 Salt bridges: B:R.215, B:H.223 SO4.24: 3 residues within 4Å: Chain C: W.82, H.83, H.84 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.83 Salt bridges: C:H.84 SO4.25: 7 residues within 4Å: Chain C: H.84, H.85, N.86 Chain D: H.84, H.85, N.86 Ligands: SO4.32 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.85, C:N.86, C:N.86, D:H.85, D:N.86 Water bridges: C:N.86, D:N.86 SO4.31: 3 residues within 4Å: Chain D: W.82, H.83, H.84 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.83 Salt bridges: D:H.84 SO4.32: 7 residues within 4Å: Chain C: H.84, H.85, N.86 Chain D: H.84, H.85, N.86 Ligands: SO4.25 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:H.85, C:N.86, D:H.85, D:N.86, D:N.86 Water bridges: C:N.86, D:N.86

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 9 residues within 4Å: Chain A: L.188, V.189, H.192, A.208, L.209, Y.211, M.213, Y.214, R.215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.211, A:M.213, A:R.215 Water bridges: A:E.207, A:Y.211 TRS.18: 9 residues within 4Å: Chain B: L.188, V.189, H.192, A.208, L.209, Y.211, M.213, Y.214, R.215 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.211, B:M.213, B:R.215 Water bridges: B:E.207, B:Y.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scannevin, R.H. et al., Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation. J. Biol. Chem. (2017)

Release Date

2017-09-13

Peptides

Matrix metalloproteinase-9: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

Matrix metalloproteinase-9

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