SMTL ID : 4efs.1

Human MMP12 in complex with L-glutamate motif inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 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: E37.6 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.2, H2O.2 CA.4: 3 residues within 4Å: Chain A: D.20, E.95, E.97 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.20, A:D.20, A:E.95, A:E.97, 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 E37: N~2~-[4-(4-phenylthiophen-2-yl)benzoyl]-L-alpha-glutamine(Non-covalent)

E37.6: 22 residues within 4Å: Chain A: G.75, I.76, L.77, A.78, L.110, T.111, H.114, E.115, H.118, H.124, P.128, K.129, A.130, V.131, F.133, P.134, T.135, Y.136, K.137 Ligands: ZN.1, PGR.9, PGO.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.77, A:T.111, A:H.114, A:F.133 Hydrogen bonds: A:A.78, A:A.78 Salt bridges: A:H.114, A:H.118, A:H.124 pi-Stacking: A:H.114

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: Y.28, A.29, T.101, N.107, F.109, I.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.107

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: H.118, G.123, H.124 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.122, A:H.124, A:H.124 EDO.13: 4 residues within 4Å: Chain A: I.14, N.15, Y.17, R.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.15, A:R.23

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

PGR.9: 3 residues within 4Å: Chain A: H.124, P.134 Ligands: E37.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.134

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

PGO.10: 6 residues within 4Å: Chain A: G.75, L.77, P.134, T.135, Y.136 Ligands: E37.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.75, A:Y.136 PGO.11: 2 residues within 4Å: Chain A: A.148, I.151 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.151 PGO.14: 5 residues within 4Å: Chain A: V.4, W.5, R.6, K.7, G.84 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.4, A:R.6

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 4 residues within 4Å: Chain A: H.68, H.79, A.80, F.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.80 Water bridges: A:G.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devel, L. et al., Simple pseudo-dipeptides with a P2' glutamate: a novel inhibitor family of matrix metalloproteases and other metzincins. J.Biol.Chem. (2012)

Release Date

2012-06-20

Peptides

Macrophage metalloelastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage metalloelastase

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