5YZH Oxidoreductase date Dec 14, 2017
title Crystal Structure Of Mouse Cytosolic Isocitrate Dehydrogenas
authors H.J.Cho, B.S.Kang
compound source
Molecule: Isocitrate Dehydrogenase [Nadp] Cytoplasmic
Chain: A, B
Synonym: Idh,Cytosolic Nadp-Isocitrate Dehydrogenase,Idp,Na Specific Icdh,Oxalosuccinate Decarboxylase;
Ec: 1.1.1.42
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Idh1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: C 1 2 1
R_factor 0.182 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.372 91.289 109.381 90.00 113.34 90.00
method X-Ray Diffractionresolution 1.99 Å
ligand GOL, NAP enzyme Oxidoreductase E.C.1.1.1.42 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNADP(+)-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione., Cho HJ, Cho HY, Park JW, Kwon OS, Lee HS, Huh TL, Kang BS, J Biol Inorg Chem. 2018 Jun 19. pii: 10.1007/s00775-018-1581-5. doi:, 10.1007/s00775-018-1581-5. PMID:29923039
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (5yzh.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 5YZH
  • CSU: Contacts of Structural Units for 5YZH
  • Structure Factors (1285 Kb)
  • Retrieve 5YZH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YZH from S2C, [Save to disk]
  • View 5YZH 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 5YZH
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yzh_B] [5yzh_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YZH
  • Community annotation for 5YZH at PDBWiki (http://pdbwiki.org)

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