1UMC Oxidoreductase date Sep 25, 2003
title Branched-Chain 2-Oxo Acid Dehydrogenase (E1) From Thermus Th Hb8 With 4-Methylpentanoate
authors T.Nakai, N.Nakagawa, N.Maoka, R.Masui, S.Kuramitsu, N.Kamiya, Rike Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: 2-Oxo Acid Dehydrogenase Alpha Subunit
Chain: A, C
Synonym: E1-Alpha
Ec: 1.2.4.4
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pacyc184

Molecule: 2-Oxo Acid Dehydrogenase Beta Subunit
Chain: B, D
Synonym: E1-Beta
Ec: 1.2.4.4
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Blr(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: C 2 2 21
R_factor 0.172 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
127.197 247.216 137.557 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 4MV, MG, TDP, TPP enzyme Oxidoreductase E.C.1.2.4.4 BRENDA
related structures by homologous chain: 1UM9
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceLigand-induced Conformational Changes and a Reaction Intermediate in Branched-chain 2-Oxo Acid Dehydrogenase (E1) from Thermus thermophilus HB8, as Revealed by X-ray Crystallography., Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N, J Mol Biol 2004 Apr 2;337(4):1011-33. PMID:15033367
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (1umc.pdb1.gz) 226 Kb
  • LPC: Ligand-Protein Contacts for 1UMC
  • CSU: Contacts of Structural Units for 1UMC
  • Likely Quarternary Molecular Structure file(s) for 1UMC
  • Structure Factors (698 Kb)
  • Retrieve 1UMC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UMC from S2C, [Save to disk]
  • Re-refined 1umc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1UMC 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 1UMC
  • 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 1UMC, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1umca_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1umcb2, region B:188-324 [Jmol] [rasmolscript] [script source]
        - Domain d1umcb1, region B:2-187 [Jmol] [rasmolscript] [script source]
        - Domain d1umcc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1umcd2, region D:188-324 [Jmol] [rasmolscript] [script source]
        - Domain d1umcd1, region D:2-187 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1umc_D] [1umc_A] [1umc] [1umc_B] [1umc_C]
  • SWISS-PROT database: [Q5SLR4] [Q5SLR3]
  • Domain organization of [ODBA_THET8] [ODBB_THET8] by SWISSPFAM
  • Domain found in 1UMC: [Transket_pyr ] by SMART
  • Other resources with information on 1UMC
  • Community annotation for 1UMC 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science