3VL6 Oxidoreductase date Nov 29, 2011
title 3-Isopropylmalate Dehydrogenase From Shewanella Oneidensis M Mpa
authors T.Nagae, N.Watanabe
compound source
Molecule: 3-Isopropylmalate Dehydrogenase
Chain: A
Synonym: 3-Ipm-Dh, Beta-Ipm Dehydrogenase, Imdh
Engineered: Yes
Organism_scientific: Shewanella Oneidensis
Organism_taxid: 211586
Strain: Mr-1
Gene: Leub, So_4235
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codonplus(De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe80
symmetry Space Group: C 1 2 1
R_factor 0.174 R_Free 0.235
length a length b length c angle alpha angle beta angle gamma
103.144 57.380 75.213 90.00 118.76 90.00
method X-Ray Diffractionresolution 2.07 Å
ligand CA, CL, IPM enzyme Oxidoreductase E.C. BRENDA
Gene SO

Primary referenceHigh-pressure-induced water penetration into 3-isopropylmalate dehydrogenase., Nagae T, Kawamura T, Chavas LM, Niwa K, Hasegawa M, Kato C, Watanabe N, Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):300-9. Epub 2012 Feb 14. PMID:22349232
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (3vl6.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 3VL6
  • CSU: Contacts of Structural Units for 3VL6
  • Structure Factors (173 Kb)
  • Retrieve 3VL6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VL6 from S2C, [Save to disk]
  • Re-refined 3vl6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VL6 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 3VL6
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3VL6, from MSDmotif at EBI
  • Fold representative 3vl6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vl6] [3vl6_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VL6: [Iso_dh ] by SMART
  • Other resources with information on 3VL6
  • Community annotation for 3VL6 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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