1SIR Oxidoreductase date Mar 01, 2004
title The Crystal Structure And Mechanism Of Human Glutaryl-Coa Dehydrogenase
authors M.Wang, Z.Fu, R.Paschke, S.L.Goodman, F.E.Frerman, J.J.Kim
compound source
Molecule: Glutaryl-Coa Dehydrogenase
Chain: A
Synonym: Gcd
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Bacterial:Bl21
symmetry Space Group: P 64 2 2
R_factor 0.187 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
116.722 116.722 128.034 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand FAD, NBC enzyme Oxidoreductase E.C. BRENDA
related structures by homologous chain: 1SIQ

Primary referenceCrystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions., Fu Z, Wang M, Paschke R, Rao KS, Frerman FE, Kim JJ, Biochemistry 2004 Aug 3;43(30):9674-84. PMID:15274622
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (1sir.pdb1.gz) 257 Kb
  • LPC: Ligand-Protein Contacts for 1SIR
  • CSU: Contacts of Structural Units for 1SIR
  • Likely Quarternary Molecular Structure file(s) for 1SIR
  • Structure Factors (116 Kb)
  • Retrieve 1SIR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SIR from S2C, [Save to disk]
  • Re-refined 1sir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SIR 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 1SIR
  • 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 1SIR, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sira1, region A:239-392 [Jmol] [rasmolscript] [script source]
        - Domain d1sira2, region A:3-238 [Jmol] [rasmolscript] [script source]
  • Fold representative 1sir from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1sir_A] [1sir]
  • SWISS-PROT database: [Q92947]
  • Domain organization of [GCDH_HUMAN] by SWISSPFAM
  • Other resources with information on 1SIR
  • Community annotation for 1SIR 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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