1T0L Oxidoreductase date Apr 10, 2004
title Crystal Structure Of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase In Complex With Nadp, Isocitrate, And Calcium(2+)
authors X.Xu, J.Zhao, B.Peng, Q.Huang, E.Arnold, J.Ding
compound source
Molecule: Isocitrate Dehydrogenase [Nadp] Cytoplasmic
Chain: A, B, C, D
Synonym: Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase, Oxalosuccinate Decarboxylase, Idh, Nadp+- Specific Icdh, Idp;
Ec: 1.1.1.42
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Idh
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b(+)
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.298 86.738 115.766 90.00 107.15 90.00
method X-Ray Diffractionresolution 2.41 Å
ligand CA, ICT, NAP enzyme Oxidoreductase E.C.1.1.1.42 BRENDA
related structures by homologous chain: 1LWD, 1T09
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity., Xu X, Zhao J, Xu Z, Peng B, Huang Q, Arnold E, Ding J, J Biol Chem 2004 Aug 6;279(32):33946-57. Epub 2004 Jun 1. PMID:15173171
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (297 Kb) [Save to disk]
  • Biological Unit Coordinates (1t0l.pdb1.gz) 147 Kb
  • Biological Unit Coordinates (1t0l.pdb2.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 1T0L
  • CSU: Contacts of Structural Units for 1T0L
  • Likely Quarternary Molecular Structure file(s) for 1T0L
  • Structure Factors (588 Kb)
  • Retrieve 1T0L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1T0L from S2C, [Save to disk]
  • Re-refined 1t0l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1T0L 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 1T0L
  • 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 1T0L, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1t0la_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1t0lb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1t0lc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1t0ld_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1t0l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1t0l_B] [1t0l_D] [1t0l] [1t0l_C] [1t0l_A]
  • SWISS-PROT database: [O75874]
  • Domain organization of [IDHC_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1T0L with the sequences similar proteins can be viewed for 1T0L's classification [IDHC_HUMAN] 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 [IDHC_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1T0L
  • Community annotation for 1T0L 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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