SMTL ID : 2w4i.2 (1 other biounit)

Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.1: 13 residues within 4Å: Chain A: D.7, S.8, V.37, P.38, Y.39, G.40, C.70, N.71, T.72, T.116, C.181, T.182, H.183 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.8, A:Y.39, A:G.40, A:N.71, A:T.72, A:T.72, A:T.182, A:T.182, A:T.182 Water bridges: A:T.119 DGL.3: 14 residues within 4Å: Chain B: D.7, S.8, V.37, P.38, Y.39, G.40, C.70, N.71, T.72, T.116, V.146, C.181, T.182, H.183 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.146 Hydrogen bonds: B:S.8, B:Y.39, B:G.40, B:N.71, B:T.72, B:T.182, B:T.182, B:T.182 Water bridges: B:G.9, B:T.119

1 x VGA: 1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-1,4-BENZODIAZEPIN-2-YL]AZETIDIN-3-OL

VGA.2: 15 residues within 4Å: Chain A: V.37, P.38, T.41, S.143, V.146, P.147, E.150, E.151 Chain B: V.37, P.38, T.41, V.146, P.147, E.150, E.151 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:V.37, A:T.41, A:P.147, A:E.150, B:V.37, B:P.38, B:V.146, B:P.147, B:E.150, B:E.150, B:E.151 Hydrogen bonds: A:E.151, A:E.151 Water bridges: A:E.150, B:S.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geng, B. et al., Potent and selective inhibitors of Helicobacter pylori glutamate racemase (MurI): pyridodiazepine amines. Bioorg. Med. Chem. Lett. (2009)

Release Date

2008-12-09

Peptides

GLUTAMATE RACEMASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

GLUTAMATE RACEMASE

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