8EB3

Crystal structure of glutamate racemase from Helicobacter pylori in complex with a fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of glutamate racemase from Helicobacter pylori in complex with a fragment

Cooling, G.T.Propp, J.Spies, M.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate racemase
A, B
260Helicobacter pyloriMutation(s): 0 
Gene Names: murIOUM_0701
EC: 5.1.1.3
UniProt
Find proteins for K2K6A3 (Helicobacter pylori R038b)
Explore K2K6A3 
Go to UniProtKB:  K2K6A3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK2K6A3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WFI (Subject of Investigation/LOI)
Query on WFI

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
1-[4-methyl-2-(pyridin-4-yl)-1,3-thiazol-5-yl]methanamine
C10 H11 N3 S
HSWRYUZXDMQDGC-UHFFFAOYSA-N
DGL
Query on DGL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
DGL BindingDB:  8EB3 Ki: 5800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.002α = 90
b = 95.985β = 112.97
c = 57.074γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM097373

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release