SMTL ID : 4h76.1

Crystal structure of the catalytic domain of Human MMP12 in complex with a broad spectrum hydroxamate inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: 10B.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 10B: N-2-(biphenyl-4-ylsulfonyl)-N-2-(isopropyloxy)-acetohydroxamic acid(Non-covalent)

10B.6: 16 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.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.114, A:Y.136 Hydrogen bonds: A:A.78, A:A.78 pi-Stacking: A:H.114

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

PGO.7: 3 residues within 4Å: Chain A: R.152, Q.155, S.156 No protein-ligand interaction detected (PLIP) PGO.8: 4 residues within 4Å: Chain A: H.68, H.79, A.80, F.81 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.79, A:F.81 Hydrogen bonds: A:H.68 PGO.9: 5 residues within 4Å: Chain A: P.3, F.81, G.82, P.83, G.88 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.81 Hydrogen bonds: A:G.82 Water bridges: A:G.88

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

PEG.10: 5 residues within 4Å: Chain A: H.118, G.121, L.122, G.123, H.124 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.121, A:H.124, A:H.124 Water bridges: A:G.2, A:G.123 PEG.11: 3 residues within 4Å: Chain A: R.61, G.62, A.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.63 PEG.12: 3 residues within 4Å: Chain A: D.25, T.101, H.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.101 Water bridges: A:T.101

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: V.4, W.5, R.6, K.7, P.83, G.84, S.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.6, A:K.7, A:P.83

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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