SMTL ID : 5w1q.1

Crystal structure of alternate isoform of glutamate racemase from Helicobacter pylori bound to D-glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

DGL.1: 15 residues within 4Å: Chain A: D.27, S.28, G.31, V.57, P.58, Y.59, G.60, C.90, N.91, T.92, T.136, V.166, C.201, T.202, H.203 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.28, A:S.28, A:Y.59, A:G.60, A:N.91, A:T.92, A:T.92, A:T.92, A:T.202 DGL.4: 14 residues within 4Å: Chain B: D.27, S.28, V.57, P.58, Y.59, G.60, C.90, N.91, T.92, T.136, V.166, C.201, T.202, H.203 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.28, B:S.28, B:Y.59, B:G.60, B:N.91, B:T.92, B:T.92, B:T.92, B:T.202 Water bridges: B:S.28

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: I.169, E.170, E.171, N.172, L.174, L.206, Q.268, E.271, W.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.169, A:N.172, A:N.172, A:W.272 GOL.3: 8 residues within 4Å: Chain A: I.173, E.175, G.176, E.177, L.178, L.179 Chain B: T.181, Y.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.175, A:L.178, A:L.179 GOL.5: 9 residues within 4Å: Chain B: I.169, E.170, E.171, N.172, L.174, L.206, Q.268, E.271, W.272 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.169, B:N.172, B:W.272 Water bridges: B:E.170 GOL.6: 8 residues within 4Å: Chain B: A.119, Q.123, L.227, I.228, H.229, D.232, A.233, E.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.123, B:Q.123, B:L.227, B:H.229 GOL.7: 7 residues within 4Å: Chain A: Y.185 Chain B: I.173, E.175, G.176, E.177, L.178, L.179 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.176, B:E.177, B:L.178, B:L.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vance, N.R. et al., Crystal structure of alternate isoform of glutamate racemase from Helicobacter pylori bound to D-glutamate. To Be Published

Release Date

2017-06-21

Peptides

Glutamate racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate racemase