SMTL ID : 8udi.1

Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a crystallographic artifact

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

DGL.1: 14 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, V.146, C.181, T.182, H.183 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.8, A:S.8, A:S.8, A:Y.39, A:G.40, A:N.71, A:T.72, A:T.182, A:T.182 Water bridges: A:S.8 DGL.4: 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.146 Hydrogen bonds: B:S.8, 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 Water bridges: B:T.119

1 x WAW: N-{[(3S)-2-(3-fluoropyrazin-2-yl)-1,2,3,4-tetrahydroisoquinolin-3-yl]methyl}-1H-indazole-4-carboxamide(Non-covalent)

WAW.2: 6 residues within 4Å: Chain A: F.236, I.243, E.246, R.247, A.249, K.250 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.247 Hydrogen bonds: A:K.250 Halogen bonds: A:E.246

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: I.149, S.152, W.252 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: I.149, S.152, L.186 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Propp, J. et al., Structure of H. Pylori Glutamate Racemace with a crystallographic artifact. To Be Published

Release Date

2024-10-09

Peptides

Glutamate racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate racemase