SMTL ID : 5h0u.1

Crystal structure of the catalytic domain of membrane type 1 matrix metalloproteinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

1 x HIS- HIS- HIS- HIS- HIS- HIS: HIS-HIS-HIS-HIS-HIS-HIS(Non-covalent)

HIS-HIS-HIS-HIS-HIS-HIS.1: 17 residues within 4Å: Chain A: T.75, F.83, A.85, H.86, A.87, Y.88, F.89, P.90, G.95, H.124, E.125, H.128, E.133, H.134 Ligands: ZN.3, GOL.12, ZN.15 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.75, A:F.83, A:Y.88, A:H.128 Hydrogen bonds: A:H.86, A:A.87, A:A.87 Water bridges: A:S.74, A:T.75, A:F.89, A:F.89, A:H.128, A:H.134 Salt bridges: A:H.124, A:H.128, A:H.134 pi-Stacking: A:F.83, A:F.89

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.61, N.93, I.94, G.95, D.97 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.61, A:N.93, A:G.95, A:D.97, H2O.2, H2O.2 CA.5: 6 residues within 4Å: Chain A: D.78, G.79, G.81, F.83, D.101, E.104 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.78, A:G.79, A:G.81, A:F.83, A:D.101, A:E.104

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.124, H.128, H.134 Ligands: HIS-HIS-HIS-HIS-HIS-HIS.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.124, A:H.128, A:H.134, H2O.1 ZN.4: 5 residues within 4Å: Chain A: H.71, D.73, H.86, Y.88, H.99 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.71, A:D.73, A:H.86, A:H.99 ZN.15: 4 residues within 4Å: Chain A: F.89, E.133 Ligands: HIS-HIS-HIS-HIS-HIS-HIS.1, HIS-HIS-HIS-HIS-HIS-HIS.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.133, A:E.133

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 3 residues within 4Å: Chain A: F.65, H.71, G.72 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: Y.16, G.21, E.22, Y.23 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.16, A:E.22, A:Y.23 Water bridges: A:G.21 GOL.8: 5 residues within 4Å: Chain A: F.11, R.30, R.34, E.37, F.44 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.30, A:F.44 GOL.9: 4 residues within 4Å: Chain A: Q.59, N.93, I.94, D.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.59, A:I.94 Water bridges: A:D.97 GOL.10: 4 residues within 4Å: Chain A: G.131, L.132, E.133, H.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.133, A:E.133 GOL.11: 5 residues within 4Å: Chain A: E.68, G.69, F.77, G.79, A.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.68, A:E.68, A:G.79 Water bridges: A:G.69 GOL.12: 9 residues within 4Å: Chain A: L.84, L.120, V.121, H.124, E.125, F.145, Y.146 Ligands: HIS-HIS-HIS-HIS-HIS-HIS.1, GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.120 Water bridges: A:P.144, A:Q.147 GOL.13: 7 residues within 4Å: Chain A: G.82, F.83, L.84, F.145, Y.146 Ligands: GOL.12, GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.84, A:Y.146 GOL.14: 4 residues within 4Å: Chain A: D.78, G.82, F.83 Ligands: GOL.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decaneto, E. et al., Solvent water interactions within the active site of the membrane type I matrix metalloproteinase. Phys Chem Chem Phys (2017)

Release Date

2017-10-04

Peptides

Matrix metalloproteinase-14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrix metalloproteinase-14