3EXH 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, E
Fragment: E1p-Alpha
Synonym: Pyruvate Dehydrogenase (E1p) Alpha Subunit; Pdhe1-
Ec: 1.2.4.1
Engineered: Yes
Mutation: Yes
Other_details: S203as271a With Bound Mn-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

Molecule: Pyruvate Dehydrogenase E1 Component Subunit Alpha Form, Mitochondrial;
Chain: C, G
Fragment: E1p-Alpha
Synonym: Pyruvate Dehydrogenase (E1p) Alpha Subunit; Pdhe1-
Ec: 1.2.4.1
Engineered: Yes
Mutation: Yes
Other_details: Phosphorylated S264, S203as271a With Bound

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
symmetry Space Group: C 1 2 1
R_factor 0.165 R_Free 0.211
crystal
cell
length a length b length c angle alpha angle beta angle gamma
257.064 115.612 127.592 90.00 113.64 90.00
method X-Ray Diffractionresolution 2.44 Å
ligand GOL, K, MN, SEP, 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] (451 Kb) [Save to disk]
  • Biological Unit Coordinates (3exh.pdb1.gz) 227 Kb
  • Biological Unit Coordinates (3exh.pdb2.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 3EXH
  • CSU: Contacts of Structural Units for 3EXH
  • Likely Quarternary Molecular Structure file(s) for 3EXH
  • Structure Factors (1996 Kb)
  • Retrieve 3EXH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EXH from S2C, [Save to disk]
  • Re-refined 3exh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EXH 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 3EXH
  • 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 3EXH, from MSDmotif at EBI
  • Fold representative 3exh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3exh_H] [3exh_C] [3exh_D] [3exh_A] [3exh_B] [3exh_G] [3exh_E] [3exh] [3exh_F]
  • SWISS-PROT database: [P08559] [P11177]
  • Domain organization of [ODPA_HUMAN] [ODPB_HUMAN] by SWISSPFAM
  • Domain found in 3EXH: [Transket_pyr ] by SMART
  • Alignments of the sequence of 3EXH with the sequences similar proteins can be viewed for 3EXH'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 3EXH
  • Community annotation for 3EXH 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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