1DIY Oxidoreductase date Nov 30, 1999
title Crystal Structure Of Arachidonic Acid Bound In The Cyclooxyg Active Site Of Pghs-1
authors M.G.Malkowski, S.L.Ginell, W.L.Smith, R.M.Garavito
compound source
Molecule: Prostaglandin H2 Synthase-1
Chain: A
Ec: 1.14.99.1
Organism_scientific: Ovis Aries
Organism_common: Sheep
Organism_taxid: 9940
Organ: Seminal Vessicle
symmetry Space Group: P 65 2 2
R_factor 0.215 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
182.100 182.100 103.640 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand ACD, BMA, BOG, COH, MAN, NAG, NDG enzyme Oxidoreductase E.C.1.14.99.1 BRENDA
related structures by homologous chain: 1CX2, 1PXX
Gene
Ontology
ChainFunctionProcessComponent
A
  • peroxidase activity


  • Primary referenceThe productive conformation of arachidonic acid bound to prostaglandin synthase., Malkowski MG, Ginell SL, Smith WL, Garavito RM, Science 2000 Sep 15;289(5486):1933-7. PMID:10988074
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (1diy.pdb1.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 1DIY
  • CSU: Contacts of Structural Units for 1DIY
  • Likely Quarternary Molecular Structure file(s) for 1DIY
  • Structure Factors (300 Kb)
  • Retrieve 1DIY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DIY from S2C, [Save to disk]
  • Re-refined 1diy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DIY 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 1DIY
  • 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 1DIY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1diya2, region A:32-73 [Jmol] [rasmolscript] [script source]
        - Domain d1diya1, region A:74-584 [Jmol] [rasmolscript] [script source]
  • Fold representative 1diy from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1diy] [1diy_A]
  • SWISS-PROT database: [P05979]
  • Domain organization of [PGH1_SHEEP] by SWISSPFAM
  • Domain found in 1DIY: [EGF ] by SMART
  • Other resources with information on 1DIY
  • Community annotation for 1DIY 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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