2D4V Oxidoreductase date Oct 24, 2005
title Crystal Structure Of Nad Dependent Isocitrate Dehydrogenase Acidithiobacillus Thiooxidans
authors K.Imada, T.Tamura, K.Namba, K.Inagaki
compound source
Molecule: Isocitrate Dehydrogenase
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Acidithiobacillus Thiooxidans
Organism_taxid: 930
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.179 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.981 125.981 267.774 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand FLC, NAD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity., Imada K, Tamura T, Takenaka R, Kobayashi I, Namba K, Inagaki K, Proteins. 2008 Jan 1;70(1):63-71. PMID:17634983
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (290 Kb) [Save to disk]
  • Biological Unit Coordinates (2d4v.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (2d4v.pdb2.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 2D4V
  • CSU: Contacts of Structural Units for 2D4V
  • Likely Quarternary Molecular Structure file(s) for 2D4V
  • Structure Factors (1235 Kb)
  • Retrieve 2D4V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D4V from S2C, [Save to disk]
  • Re-refined 2d4v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2D4V in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 2D4V
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2D4V, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d4v_D] [2d4v_B] [2d4v_C] [2d4v] [2d4v_A]
  • SWISS-PROT database: [Q8GAX0]
  • Domain organization of [Q8GAX0_THITH] by SWISSPFAM
  • Domain found in 2D4V: [Iso_dh ] by SMART
    • Other resources with information on 2D4V
  • Community annotation for 2D4V at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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