2JFZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 2JFZ

Classification: ISOMERASE

Total Structure Weight: 58237.66

Macromolecule Entities
Molecule Chains Length Organism Details
GLUTAMATE RACEMASE A, B 255 Helicobacter pylori EC#: 5.1.1.3 IUBMB
Gene Name(s): murI glr jhp_0496
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
003
Query on 003

A, B 5-METHYL-7-(2-METHYLPROPYL)-2-(NAPHTHALEN- 1-YLMETHYL)-3-PYRIDIN-4-YL-2H-PYRAZOLO[3,4- D]PYRIMIDINE-4,6(5H,7H)-DIONE
C26 H25 N5 O2
NNZDBCPMOOEFTE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DGL
Query on DGL

A, B D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
003 IC50: 1400 nM (93) BindingDB
Kd: 2900 - 3900 nM (93) BindingDB

Ki: 5800 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.206
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 61.41 α = 90.00
b = 76.31 β = 90.00
c = 108.92 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-06
  • Released Date: 2007-07-03
  • Deposition author(s): Lundqvist, T.

Revision History

  • Version 1_0: 2007-07-03

    Type: Initial release

  • Version 1_1: 2011-05-08

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance