1UDY Oxidoreductase date May 07, 2003
title Medium-Chain Acyl-Coa Dehydrogenase With 3-Thiaoctanoyl-Coa
authors A.Satoh, Y.Nakajima, I.Miyahara, K.Hirotsu, T.Tanaka, Y.Nishina, K H.Tamaoki, C.Setoyama, R.Miura
compound source
Molecule: Acyl-Coa Dehydrogenase, Medium-Chain Specific
Chain: A, B, C, D
Synonym: Medium-Chain Acyl-Coa Dehydrogenase
Ec: 1.3.99.3
 Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Tissue: Liver
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.000 110.600 147.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CS8, FAD enzyme Oxidoreductase E.C.1.3.99.3 BRENDA
related structures by homologous chain: 1EGD, 3MDE
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA., Satoh A, Nakajima Y, Miyahara I, Hirotsu K, Tanaka T, Nishina Y, Shiga K, Tamaoki H, Setoyama C, Miura R, J Biochem (Tokyo) 2003 Aug;134(2):297-304. PMID:12966080
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (254 Kb) [Save to disk]
  • Biological Unit Coordinates (1udy.pdb1.gz) 247 Kb
  • LPC: Ligand-Protein Contacts for 1UDY
  • CSU: Contacts of Structural Units for 1UDY
  • Likely Quarternary Molecular Structure file(s) for 1UDY
  • Structure Factors (534 Kb)
  • Retrieve 1UDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UDY from S2C, [Save to disk]
  • Re-refined 1udy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1UDY 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 1UDY
  • 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 1UDY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1udya2, region A:11-241 [Jmol] [rasmolscript] [script source]
        - Domain d1udya1, region A:242-395 [Jmol] [rasmolscript] [script source]
        - Domain d1udyb2, region B:11-241 [Jmol] [rasmolscript] [script source]
        - Domain d1udyb1, region B:242-393 [Jmol] [rasmolscript] [script source]
        - Domain d1udyc2, region C:11-241 [Jmol] [rasmolscript] [script source]
        - Domain d1udyc1, region C:242-395 [Jmol] [rasmolscript] [script source]
        - Domain d1udyd2, region D:11-241 [Jmol] [rasmolscript] [script source]
        - Domain d1udyd1, region D:242-395 [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: [1udy_D] [1udy_A] [1udy_C] [1udy] [1udy_B]
  • SWISS-PROT database: [P41367]
  • Domain organization of [ACADM_PIG] by SWISSPFAM
    • Other resources with information on 1UDY
  • Community annotation for 1UDY 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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