SMTL ID : 4h84.2 (1 other biounit)

Crystal structure of the catalytic domain of Human MMP12 in complex with a selective carboxylate based inhibitor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x Y38: N-[2-(benzoylamino)ethyl]-N-(biphenyl-4-ylsulfonyl)-D-valine(Non-covalent)

Y38.1: 17 residues within 4Å: Chain A: I.76, L.77, A.78, H.79, L.110, T.111, H.114, E.115, H.118, H.124, V.131, F.133, P.134, T.135, Y.136 Ligands: ZN.2, GOL.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.76, A:H.79, A:H.114, A:Y.136 Hydrogen bonds: A:L.77, A:A.78, A:A.78 Salt bridges: A:H.114, A:H.118, A:H.124

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: Y38.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.3: 4 residues within 4Å: Chain A: H.64, D.66, H.79, H.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.64, A:D.66, A:H.79, A:H.92

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.54, G.86, I.87, G.88, D.90 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.54, A:G.86, A:G.88, A:D.90, H2O.1 CA.5: 3 residues within 4Å: Chain A: D.20, E.95, E.97 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:E.95, A:E.95, H2O.1, H2O.1 CA.6: 6 residues within 4Å: Chain A: D.71, G.72, G.74, I.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.71, A:G.72, A:G.74, A:I.76, A:D.94, A:E.97

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

PGO.7: 3 residues within 4Å: Chain A: D.71, K.73, G.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.71, A:K.73 PGO.8: 6 residues within 4Å: Chain A: Y.28, A.29, K.32, T.101, F.109, I.141 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.109, A:I.141 Hydrogen bonds: A:Y.28 Water bridges: A:A.29, A:A.29 PGO.12: 2 residues within 4Å: Chain A: I.141, F.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.144

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: K.129, A.130, V.131, T.135, K.137 Ligands: Y38.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.129, A:T.135, A:K.137 Water bridges: A:V.131 GOL.10: 6 residues within 4Å: Chain A: V.4, W.5, R.6, K.7, P.83, G.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.6, A:K.7, A:P.83 Water bridges: A:V.4 GOL.11: 3 residues within 4Å: Chain A: P.42, Y.158, G.159 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.158

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

2013-04-24

Peptides

Macrophage metalloelastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Macrophage metalloelastase

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