3INM Oxidoreductase date Aug 12, 2009
title Crystal Structure Of Human Cytosolic Nadp(+)-Dependent Isoci Dehydrogenase R132h Mutant In Complex With Nadph, Alpha-Ket And Calcium(2+)
authors E.Fontano, R.S.Brown, R.K.Suto, B.Bhyravbhatla
compound source
Molecule: Isocitrate Dehydrogenase [Nadp] Cytoplasmic
Chain: A, B, C
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: Pet-41a(+)
symmetry Space Group: C 2 2 21
R_factor 0.220 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
96.120 274.690 116.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand AKG, CA, GOL, NA, NDP enzyme Oxidoreductase E.C. BRENDA
A, C, B

Primary referenceCancer-associated IDH1 mutations produce 2-hydroxyglutarate., Dang L, White DW, Gross S, Bennett BD, Bittinger MA, Driggers EM, Fantin VR, Jang HG, Jin S, Keenan MC, Marks KM, Prins RM, Ward PS, Yen KE, Liau LM, Rabinowitz JD, Cantley LC, Thompson CB, Vander Heiden MG, Su SM, Nature. 2009 Dec 10;462(7274):739-44. Epub . PMID:19935646
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (212 Kb) [Save to disk]
  • Biological Unit Coordinates (3inm.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (3inm.pdb2.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 3INM
  • CSU: Contacts of Structural Units for 3INM
  • Structure Factors (1284 Kb)
  • Retrieve 3INM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3INM from S2C, [Save to disk]
  • Re-refined 3inm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3INM 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 3INM
  • 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 3INM, from MSDmotif at EBI
  • Fold representative 3inm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3inm_C] [3inm_A] [3inm_B] [3inm]
  • SWISS-PROT database: [O75874]
  • Domain organization of [IDHC_HUMAN] by SWISSPFAM
  • Domain found in 3INM: [Iso_dh ] by SMART
  • Other resources with information on 3INM
  • Community annotation for 3INM 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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