3MAP Oxidoreductase date Mar 24, 2010
title Crystal Structure Of Homodimeric R132h Mutant Of Human Cytos Nadp(+)-Dependent Isocitrate Dehydrogenase In Complex With Isocitrate
authors B.Yang, Y.Peng, J.Ding
compound source
Molecule: Isocitrate Dehydrogenase [Nadp] Cytoplasmic
Chain: A, B
Synonym: Idh, Cytosolic Nadp-Isocitrate Dehydrogenase, Oxal Decarboxylase, Nadp(+)-Specific Icdh, Idp;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Idh1, Picd
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsf-Duet
symmetry Space Group: P 43 21 2
R_factor 0.224 R_Free 0.269
length a length b length c angle alpha angle beta angle gamma
79.836 79.836 295.956 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ICT, NAP enzyme Oxidoreductase E.C. BRENDA
A, B

Primary referenceMolecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H., Yang B, Zhong C, Peng Y, Lai Z, Ding J, Cell Res. 2010 Nov;20(11):1188-200. Epub 2010 Oct 26. PMID:20975740
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (271 Kb) [Save to disk]
  • Biological Unit Coordinates (3map.pdb1.gz) 264 Kb
  • LPC: Ligand-Protein Contacts for 3MAP
  • CSU: Contacts of Structural Units for 3MAP
  • Structure Factors (278 Kb)
  • Retrieve 3MAP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MAP from S2C, [Save to disk]
  • Re-refined 3map structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MAP in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3MAP
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  • 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 3MAP, from MSDmotif at EBI
  • Fold representative 3map from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3map] [3map_B] [3map_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3MAP with the sequences similar proteins can be viewed for 3MAP's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3MAP
  • Community annotation for 3MAP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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