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 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Minasov, G.Wawrzak, Z.Skarina, T.Onopriyenko, O.Papazisi, L.Savchenko, A.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyoxylate/hydroxypyruvate reductase AA, B, C, D315Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: ghrASTM1135ycdW
EC: 1.1.1.79 (PDB Primary Data), 1.1.1.81 (PDB Primary Data)
Find proteins for Q8ZQ30 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZQ30 
Go to UniProtKB:  Q8ZQ30
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
B, D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NDB
Query on NDB

Download CCD File 
A
N-(2-hydroxyethyl)-N,N-dimethyl-3-sulfopropan-1-aminium
C7 H18 N O4 S
CNXPCGBLGHKAIL-UHFFFAOYSA-O
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 279.621α = 90
b = 45.585β = 101.58
c = 112.335γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description