SMTL ID : 2jfz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x 003: 5-METHYL-7-(2-METHYLPROPYL)-2-(NAPHTHALEN-1-YLMETHYL)-3-PYRIDIN-4-YL-2H-PYRAZOLO[3,4-D]PYRIMIDINE-4,6(5H,7H)-DIONE(Non-covalent)

003.1: 13 residues within 4Å: Chain A: V.10, G.11, F.13, S.14, I.149, E.150, S.152, L.154, T.182, H.183, L.186, Q.248, W.252 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.10, A:V.10, A:F.13, A:E.150, A:L.186 Water bridges: A:S.152 pi-Stacking: A:H.183, A:W.252, A:W.252, A:W.252 003.3: 13 residues within 4Å: Chain B: V.10, G.11, F.13, K.17, I.149, E.150, S.152, L.154, T.182, H.183, L.186, Q.248, W.252 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.10, B:V.10, B:K.17, B:E.150, B:L.186, B:L.186, B:W.252 pi-Stacking: B:H.183, B:W.252, B:W.252, B:W.252

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

DGL.2: 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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.8, A:S.8, A:Y.39, A:G.40, A:N.71, A:T.72, A:T.72, A:T.72, A:T.182, A:T.182 Water bridges: A:G.9, A:T.119 DGL.4: 13 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, C.181, T.182, H.183 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.8, B:S.8, B:Y.39, B:G.40, B:N.71, B:T.72, B:T.72, B:T.116, B:T.182, B:T.182 Water bridges: B:G.9, B:T.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lundqvist, T. et al., Exploitation of Structural and Regulatory Diversity in Glutamate Racemases. Nature (2007)

Release Date

2007-07-03

Peptides

GLUTAMATE RACEMASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GLUTAMATE RACEMASE

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