3EXG 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, I, K, M, O, Q, S, U, W, Y, 1, 3, 5
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 The Site 1 Being Phosphorylated. Apo For
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, J, L, N, P, R, T, V, X, Z, 2, 4, 6
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
R_factor 0.189 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.278 128.290 228.410 90.14 90.05 90.02
method X-Ray Diffractionresolution 3.01 Å
ligand K enzyme Oxidoreductase E.C.1.2.4.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, T, N, 2, V, Z, L, 6, J, X, P, B, H, 4, D, R


S, K, Y, E, Q, 1, M, C, A, O, W, 3, I, G, U, 5


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] (1664 Kb) [Save to disk]
  • Biological Unit Coordinates (3exg.pdb1.gz) 223 Kb
  • Biological Unit Coordinates (3exg.pdb2.gz) 223 Kb
  • Biological Unit Coordinates (3exg.pdb3.gz) 224 Kb
  • Biological Unit Coordinates (3exg.pdb4.gz) 221 Kb
  • Biological Unit Coordinates (3exg.pdb5.gz) 223 Kb
  • Biological Unit Coordinates (3exg.pdb6.gz) 225 Kb
  • Biological Unit Coordinates (3exg.pdb7.gz) 223 Kb
  • Biological Unit Coordinates (3exg.pdb8.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 3EXG
  • CSU: Contacts of Structural Units for 3EXG
  • Likely Quarternary Molecular Structure file(s) for 3EXG
  • Structure Factors (4218 Kb)
  • Retrieve 3EXG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EXG from S2C, [Save to disk]
  • Re-refined 3exg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EXG 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 3EXG
  • 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 3EXG, from MSDmotif at EBI
  • Fold representative 3exg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3exg_R] [3exg_U] [3exg_A] [3exg_M] [3exg_X] [3exg_H] [3exg_G] [3exg_F] [3exg_4] [3exg_6] [3exg_P] [3exg_L] [3exg_S] [3exg_1] [3exg_Z] [3exg_T] [3exg_B] [3exg_O] [3exg_D] [3exg_5] [3exg_E] [3exg_W] [3exg_J] [3exg_Q] [3exg_I] [3exg_N] [3exg_3] [3exg_V] [3exg_K] [3exg] [3exg_2] [3exg_Y] [3exg_C]
  • SWISS-PROT database: [P08559] [P11177]
  • Domain organization of [ODPA_HUMAN] [ODPB_HUMAN] by SWISSPFAM
  • Domain found in 3EXG: [Transket_pyr ] by SMART
  • Alignments of the sequence of 3EXG with the sequences similar proteins can be viewed for 3EXG'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 3EXG
  • Community annotation for 3EXG 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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