3KBO

2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 3KBO

Classification: OXIDOREDUCTASE

Total Structure Weight: 146836.52

Macromolecule Entities
Molecule Chains Length Organism Details
Glyoxylate/hydroxypyruvate reductase A A, B, C, D 315 Salmonella enterica EC#: 1.1.1.79 IUBMB 1.1.1.81 IUBMB
Gene Name(s): ghrA STM1135
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDP
Query on NDP

A, B, C, D NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

B, D 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDB
Query on NDB

A N-(2-hydroxyethyl)-N,N-dimethyl-3-sulfopropan- 1-aminium
C7 H18 N O4 S
CNXPCGBLGHKAIL-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 279.62 α = 90.00
b = 45.58 β = 101.58
c = 112.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-20
  • Released Date: 2009-10-27
  • Deposition author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • Version 1_0: 2009-10-27

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Refinement description, Version format compliance