SMTL ID : 8tba.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

1 x ZMX: (2M)-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-2-[5-(4-methylphenyl)-1,3-oxazol-2-yl]benzamide(Non-covalent)

ZMX.1: 8 residues within 4Å: Chain A: L.21, V.235, F.237, I.244, E.247, R.248, K.251, L.254 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.21, A:F.237, A:I.244, A:E.247, A:L.254, A:L.254 Hydrogen bonds: A:E.247, A:E.247, A:K.251 pi-Stacking: A:F.237

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

DGL.2: 14 residues within 4Å: Chain A: D.8, S.9, V.38, P.39, Y.40, G.41, C.71, N.72, T.73, T.117, V.147, C.182, T.183, H.184 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.9, A:S.9, A:S.9, A:Y.40, A:G.41, A:N.72, A:T.73, A:T.183, A:T.183 DGL.4: 14 residues within 4Å: Chain B: D.8, S.9, V.38, P.39, Y.40, G.41, C.71, N.72, T.73, T.117, V.147, C.182, T.183, H.184 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.9, B:S.9, B:Y.40, B:G.41, B:N.72, B:T.73, B:T.73, B:T.73, B:T.183, B:T.183 Water bridges: B:G.10, B:T.120

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: I.150, S.153, L.155, L.187, E.252, W.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.153 DMS.5: 8 residues within 4Å: Chain B: I.150, E.151, S.153, L.155, L.187, Q.249, E.252, W.253 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:W.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Propp, J. et al., Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a likely crystallographic artifact. To Be Published

Release Date

2024-07-03

Peptides

Glutamate racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate racemase