SMTL ID : 3tvc.1

Human MMP13 in complex with L-glutamate motif inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: E3P.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102, H2O.3 CA.4: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102 CA.5: 5 residues within 4Å: Chain A: D.59, N.91, Y.92, G.93, D.95 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.1, H2O.3

1 x E3P: N~2~-[3-(1,1':4',1''-terphenyl-4-yl)propanoyl]-L-alpha-glutamine(Non-covalent)

E3P.6: 20 residues within 4Å: Chain A: L.81, L.82, A.83, L.115, V.116, H.119, E.120, H.123, H.129, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, T.144, F.149, P.152 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.115, A:V.116, A:H.119, A:L.136, A:Y.141, A:T.144, A:P.152 Hydrogen bonds: A:A.83 Salt bridges: A:H.119, A:H.123, A:H.129 pi-Stacking: A:H.119, A:F.149

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

PEG.7: 4 residues within 4Å: Chain A: S.108, K.109, G.110, Y.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.110 PEG.8: 5 residues within 4Å: Chain A: K.40, V.41, D.44, F.149, L.151 No protein-ligand interaction detected (PLIP) PEG.9: 5 residues within 4Å: Chain A: K.9, W.10, S.11, P.88, G.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.11 Water bridges: A:K.9

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

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Collagenase 3

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