3FKR

Structure of L-2-keto-3-deoxyarabonate dehydratase complex with pyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of L -2-keto-3-deoxyarabonate dehydratase an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism in complex with pyruvate

Shimada, N.Mikami, B.Watanabe, S.Kodaki, T.Makino, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-2-keto-3-deoxyarabonate dehydratase
A, B
309Azospirillum brasilenseGene Names: araD
EC: 4.2.1.43
Find proteins for Q1JUQ0 (Azospirillum brasilense)
Go to UniProtKB:  Q1JUQ0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KPI
Query on KPI
A, B
L-peptide linkingC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.259α = 90.00
b = 79.259β = 90.00
c = 206.527γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
PROCESSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description