2DUA

Crystal Structure of Phosphonopyruvate Hydrolase Complex with Oxalate and Mg++

Structural Biology Knowledgebase: 2DUA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.156

Literature

Macromolecules
Sequence Display for 2DUA

Classification: hydrolase

Total Structure Weight: 31572.31

Macromolecule Entities
Molecule Chains Length Organism Details
Phosphonopyruvate hydrolase A 290 Variovorax sp. pal2 EC#: 3.11.1.3 IUBMB
Gene Name(s): pphA palA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XYS
Query on XYS

A XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXL
Query on OXL

A OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
OXL N/A in BindingDB
Ki: 2000000 nM  BindingMOAD
Ki: 17000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.156
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.89 α = 90.00
b = 79.18 β = 90.00
c = 93.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-07-21
  • Released Date: 2006-10-03
  • Deposition author(s): Herzberg, O., Chen, C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name