3MAR Oxidoreductase date Mar 24, 2010
title Crystal Structure Of Homodimeric R132h Mutant Of Human Cytos Nadp(+)-Dependent Isocitrate Dehydrogenase In Complex With
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 0.245 R_Free 0.289
length a length b length c angle alpha angle beta angle gamma
83.099 83.099 306.116 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.41 Å
ligand 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] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (3mar.pdb1.gz) 119 Kb
  • LPC: Ligand-Protein Contacts for 3MAR
  • CSU: Contacts of Structural Units for 3MAR
  • Structure Factors (114 Kb)
  • Retrieve 3MAR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MAR from S2C, [Save to disk]
  • Re-refined 3mar structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MAR 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 3MAR
  • 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 3MAR, from MSDmotif at EBI
  • Fold representative 3mar from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mar_B] [3mar_A] [3mar]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3MAR with the sequences similar proteins can be viewed for 3MAR'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 3MAR
  • Community annotation for 3MAR 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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