2DUB Lyase date Apr 28, 1997
title Enoyl-Coa Hydratase Complexed With Octanoyl-Coa
authors C.K.Engel, R.K.Wierenga
compound source
Molecule: 2-Enoyl-Coa Hydratase
Chain: A, B, C, D, E, F
Synonym: Crotonase, Enoyl-Coa Hydratase 1
Ec: 4.2.1.17
Other_details: Cocrystallized With Octanoyl-Coa
 Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Organ: Liver
Cellular_location: Mitochondria
symmetry Space Group: P 21 21 21
R_factor 0.204 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.240 93.930 246.980 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CO8 enzyme Lyase E.C.4.2.1.17 BRENDA
related structures by homologous chain: 1DUB, 1EY3
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceThe crystal structure of enoyl-CoA hydratase complexed with octanoyl-CoA reveals the structural adaptations required for binding of a long chain fatty acid-CoA molecule., Engel CK, Kiema TR, Hiltunen JK, Wierenga RK, J Mol Biol 1998 Feb 6;275(5):847-59. PMID:9480773
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (2dub.pdb1.gz) 243 Kb
  • Biological Unit Coordinates (2dub.pdb2.gz) 243 Kb
  • LPC: Ligand-Protein Contacts for 2DUB
  • CSU: Contacts of Structural Units for 2DUB
  • Likely Quarternary Molecular Structure file(s) for 2DUB
  • Structure Factors (1139 Kb)
  • Retrieve 2DUB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DUB from S2C, [Save to disk]
  • Re-refined 2dub structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2DUB 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 2DUB
  • 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 2DUB, from MSDmotif at EBI
  • Genome occurence of 2DUB's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2duba_, region A [Jmol] [rasmolscript] [script source]
        - Domain d2dubb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d2dubc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d2dubd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d2dube_, region E [Jmol] [rasmolscript] [script source]
        - Domain d2dubf_, region F [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: [2dub] [2dub_C] [2dub_E] [2dub_F] [2dub_B] [2dub_A] [2dub_D]
  • SWISS-PROT database: [P14604]
  • Domain organization of [ECHM_RAT] by SWISSPFAM
    • Other resources with information on 2DUB
  • Community annotation for 2DUB 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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