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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: Y38.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.2: 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.3: 5 residues within 4Å: Chain A: D.54, G.86, I.87, G.88, D.90 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:G.86, A:G.88, A:D.90, H2O.1, H2O.1 CA.4: 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.3 CA.5: 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

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

Y38.6: 18 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, K.137 Ligands: ZN.1, PGO.14 11 PLIP interactions: 11 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 pi-Stacking: A:H.114

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

PGO.7: 2 residues within 4Å: Chain A: D.67, H.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.67 PGO.9: 5 residues within 4Å: Chain A: M.1, G.2, P.3, V.4, R.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.4, A:R.6, A:R.6 PGO.11: 5 residues within 4Å: Chain A: K.7, T.11, M.52, A.53, D.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.7, A:K.7, A:M.52 Water bridges: A:T.11, A:T.11, A:D.54 PGO.14: 5 residues within 4Å: Chain A: G.75, L.77, T.135, Y.136 Ligands: Y38.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.75, A:Y.136

1 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.8: 4 residues within 4Å: Chain A: L.77, G.105, T.106, Y.136 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.77, A:Y.136 Hydrogen bonds: A:T.106 Water bridges: A:T.106

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain A: S.85, G.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.85 GOL.15: 1 residues within 4Å: Chain A: P.19 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.61 GOL.16: 1 residues within 4Å: Chain A: R.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.23 GOL.17: 5 residues within 4Å: Chain A: V.4, W.5, R.6, K.7, G.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.4, A:R.6, A:K.7, A:G.84

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

PEG.12: 3 residues within 4Å: Chain A: G.121, G.123, H.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.121, A:H.124 Water bridges: A:H.124 PEG.13: 2 residues within 4Å: Chain A: R.6, H.8 No protein-ligand interaction detected (PLIP) PEG.18: 4 residues within 4Å: Chain A: Y.28, T.101, F.109, I.141 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.107

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
A

Macrophage metalloelastase

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