3EXF Oxidoreductase date Oct 16, 2008
title Crystal Structure Of The Pyruvate Dehydrogenase (E1p) Compon Human Pyruvate Dehydrogenase Complex
authors M.Kato, R.M.Wynn, J.L.Chuang, S.C.Tso, M.Machius, J.Li, D.T.Chuan
compound source
Molecule: Pyruvate Dehydrogenase E1 Component Subunit Alpha Form, Mitochondrial;
Chain: A, C, E, G
Fragment: E1p-Alpha
Synonym: Pyruvate Dehydrogenase (E1p) Alpha Subunit; Pdhe1-
Ec: 1.2.4.1
Engineered: Yes
Mutation: Yes
Other_details: Phosphorylation Site 1 (S264) Only Mutant (S203as271a) With Bound Mg-Thdp;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdha1, Phe1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Pyruvate Dehydrogenase E1 Component Subunit Beta, Mitochondrial;
Chain: B, D, F, H
Fragment: E1p-Beta
Synonym: Pyruvate Dehydrogenase (E1p) Beta Subunit; Pdhe1-B
Ec: 1.2.4.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdhb, Phe1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.185 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.389 129.668 144.946 90.00 109.15 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand K, MG, TPP enzyme Oxidoreductase E.C.1.2.4.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, E, C, G


F, B, H, D


Primary referenceStructural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops., Kato M, Wynn RM, Chuang JL, Tso SC, Machius M, Li J, Chuang DT, Structure. 2008 Dec 12;16(12):1849-59. PMID:19081061
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (435 Kb) [Save to disk]
  • Biological Unit Coordinates (3exf.pdb1.gz) 217 Kb
  • Biological Unit Coordinates (3exf.pdb2.gz) 217 Kb
  • LPC: Ligand-Protein Contacts for 3EXF
  • CSU: Contacts of Structural Units for 3EXF
  • Likely Quarternary Molecular Structure file(s) for 3EXF
  • Structure Factors (1141 Kb)
  • Retrieve 3EXF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EXF from S2C, [Save to disk]
  • Re-refined 3exf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EXF 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 3EXF
  • 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 3EXF, from MSDmotif at EBI
  • Fold representative 3exf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3exf_G] [3exf] [3exf_B] [3exf_A] [3exf_C] [3exf_E] [3exf_D] [3exf_F] [3exf_H]
  • SWISS-PROT database: [P08559] [P11177]
  • Domain organization of [ODPA_HUMAN] [ODPB_HUMAN] by SWISSPFAM
  • Domain found in 3EXF: [Transket_pyr ] by SMART
  • Alignments of the sequence of 3EXF with the sequences similar proteins can be viewed for 3EXF's classification [ODPA_HUMAN] [ODPB_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 [ODPA_HUMAN] [ODPB_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3EXF
  • Community annotation for 3EXF at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science