2J9F Oxidoreductase date Nov 07, 2006
title Human Branched-Chain Alpha-Ketoacid Dehydrogenase-Decarboxyl
authors L.Jun, M.Machius, J.L.Chuang, R.M.Wynn, D.T.Chuang
compound source
Molecule: 2-Oxoisovalerate Dehydrogenase Alpha Subunit
Chain: A, C
Synonym: Branched-Chain Alpha-Keto Acid Dehydrogenase E1 Co Alpha Chain, Bckdh E1-Alpha, Bckde1a;
Ec: 1.2.4.4
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrchisb (Invitrogen)
Expression_system_plasmid: Ptrc-Alpha-Betahis

Molecule: 2-Oxoisovalerate Dehydrogenase Beta Subunit
Chain: B, D
Synonym: Branched-Chain Alpha-Keto Acid Dehydrogenase E1 Co Beta Chain, Bckdh E1-Beta;
Ec: 1.2.4.4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_vector: Ptrchisb (Invitrogen)
Expression_system_plasmid: Ptrc-Alpha-Betahis
symmetry Space Group: P 32 2 1
R_factor 0.170 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.342 145.342 138.050 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.88 Å
ligand GOL, K, MN, THV enzyme Oxidoreductase E.C.1.2.4.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceThe two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism., Li J, Machius M, Chuang JL, Wynn RM, Chuang DT, J Biol Chem. 2007 Apr 20;282(16):11904-13. Epub 2007 Feb 27. PMID:17329260
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (256 Kb) [Save to disk]
  • Biological Unit Coordinates (2j9f.pdb1.gz) 248 Kb
  • LPC: Ligand-Protein Contacts for 2J9F
  • CSU: Contacts of Structural Units for 2J9F
  • Structure Factors (1074 Kb)
  • Retrieve 2J9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2J9F from S2C, [Save to disk]
  • Re-refined 2j9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2J9F 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 2J9F
  • 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
  • 3D motif for 2J9F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2j9f_A] [2j9f_C] [2j9f] [2j9f_B] [2j9f_D]
  • SWISS-PROT database: [P12694] [P21953]
  • Domain organization of [ODBA_HUMAN] [ODBB_HUMAN] by SWISSPFAM
  • Domain found in 2J9F: [Transket_pyr ] by SMART
  • Other resources with information on 2J9F
  • Community annotation for 2J9F 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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