1IYI Isomerase date Aug 26, 2002
title Crystal Structure Of Hematopoietic Prostaglandin D Synthase
authors T.Inoue
compound source
Molecule: Hematopoietic Prostaglandin D Synthase
Chain: A, B, C, D
Ec: 5.3.99.2
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.188 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.784 47.263 183.810 90.00 97.83 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CA, GSH enzyme Isomerase E.C.5.3.99.2 BRENDA
related structures by homologous chain: 1IYH, 1V40
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceMechanism of metal activation of human hematopoietic prostaglandin D synthase., Inoue T, Irikura D, Okazaki N, Kinugasa S, Matsumura H, Uodome N, Yamamoto M, Kumasaka T, Miyano M, Kai Y, Urade Y, Nat Struct Biol 2003 Apr;10(4):291-6. PMID:12627223
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (1iyi.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (1iyi.pdb2.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 1IYI
  • CSU: Contacts of Structural Units for 1IYI
  • Likely Quarternary Molecular Structure file(s) for 1IYI
  • Structure Factors (830 Kb)
  • Retrieve 1IYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IYI from S2C, [Save to disk]
  • Re-refined 1iyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1IYI 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 1IYI
  • 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 1IYI, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1iyia2, region A:2-75 [Jmol] [rasmolscript] [script source]
        - Domain d1iyia1, region A:76-199 [Jmol] [rasmolscript] [script source]
        - Domain d1iyib2, region B:202-275 [Jmol] [rasmolscript] [script source]
        - Domain d1iyib1, region B:276-399 [Jmol] [rasmolscript] [script source]
        - Domain d1iyic2, region C:402-475 [Jmol] [rasmolscript] [script source]
        - Domain d1iyic1, region C:476-599 [Jmol] [rasmolscript] [script source]
        - Domain d1iyid2, region D:602-675 [Jmol] [rasmolscript] [script source]
        - Domain d1iyid1, region D:676-799 [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: [1iyi_D] [1iyi_A] [1iyi] [1iyi_C] [1iyi_B]
  • SWISS-PROT database: [O60760]
  • Domain organization of [HPGDS_HUMAN] by SWISSPFAM
    • Other resources with information on 1IYI
  • Community annotation for 1IYI 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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