1PT8

Crystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA

Structural Biology Knowledgebase: 1PT8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 1PT8

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 99082.26

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical protein yfdW A, B 437 Escherichia coli Shigella flexneri EC#: 2.8.3.16 IUBMB
Gene Name(s): frc yfdW b2374 JW2371
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXL
Query on OXL

A, B OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.181
  • Space Group: P 62
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.79 α = 90.00
b = 146.79 β = 90.00
c = 129.90 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-23
  • Released Date: 2003-09-09
  • Deposition author(s): Gruez, A., Roig-Zamboni, V., Valencia, C., Campanacci, V., Cambillau, C.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4