5GRF Oxidoreductase date Aug 11, 2016
title Crystal Structure Of The Alpha Gamma Mutant (Gamma-K151a) Of Idh3 In Complex With Mg(2+), Citrate And Adp
authors T.Ma, J.Ding
compound source
Molecule: Isocitrate Dehydrogenase [Nad] Subunit Alpha, Mitochondrial;
Chain: A
Synonym: Isocitric Dehydrogenase Subunit Alpha,Nad(+)-Speci Subunit Alpha;
Ec: 1.1.1.41
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Idh3a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Isocitrate Dehydrogenase [Nad] Subunit Gamma, Mitochondrial;
Chain: B
Synonym: Isocitric Dehydrogenase Subunit Gamma,Nad(+)-Speci Subunit Gamma;
Ec: 1.1.1.41
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Idh3g
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 31 2 1
R_factor 0.207 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.336 114.336 143.901 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand ADP, CIT, MG enzyme Oxidoreductase E.C.1.1.1.41 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceMolecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase., Ma T, Peng Y, Huang W, Ding J, Sci Rep. 2017 Jan 18;7:40921. doi: 10.1038/srep40921. PMID:28098230
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (5grf.pdb1.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 5GRF
  • CSU: Contacts of Structural Units for 5GRF
  • Structure Factors (630 Kb)
  • Retrieve 5GRF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GRF from S2C, [Save to disk]
  • Re-refined 5grf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5GRF 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 5GRF
  • 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
  • Fold representative 5grf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5grf_A] [5grf_B] [5grf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5GRF
  • Community annotation for 5GRF at PDBWiki (http://pdbwiki.org)

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