1RY8 Oxidoreductase date Dec 19, 2003
title Prostaglandin F Synthase Complexed With Nadph And Rutin
authors J.Komoto, T.Yamada, K.Watanabe, F.Takusagawa
compound source
Molecule: Aldo-Keto Reductase Family 1 Member C3
Chain: A, B
Synonym: Akr1c3, Trans-1,2-Dihydrobenzene-1,2-Diol Dehydrog Chlordecone Reductase Homolog Hakrb, Ha1753, Dihydrodiol Dehydrogenase, Type I, Dihydrodiol Dehydrogenase 3, Dd3, 3- Hydroxysteroid Dehydrogenase, 3alpha-Hsd, Prostaglandin F S
Ec: 1.1.1.-, 1.3.1.20, 1.1.1.188
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Akr1c3, Ddh1, Pgfs, Kiaa0119
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.205 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.060 49.370 83.590 73.90 86.30 69.90
method X-Ray Diffractionresolution 1.69 Å
ligand NDP, RUT enzyme Oxidoreductase E.C.1.1.1 BRENDA
related structures by homologous chain: 1MRQ, 1RY0
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • NADP-retinol dehydrogenase a...


  • Primary referenceCrystal structure of human prostaglandin F synthase (AKR1C3)., Komoto J, Yamada T, Watanabe K, Takusagawa F, Biochemistry 2004 Mar 2;43(8):2188-98. PMID:14979715
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (1ry8.pdb1.gz) 60 Kb
  • Biological Unit Coordinates (1ry8.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1RY8
  • CSU: Contacts of Structural Units for 1RY8
  • Likely Quarternary Molecular Structure file(s) for 1RY8
  • Structure Factors (681 Kb)
  • Retrieve 1RY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RY8 from S2C, [Save to disk]
  • Re-refined 1ry8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RY8 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 1RY8
  • 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 1RY8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ry8a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ry8b_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1ry8 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: [1ry8] [1ry8_A] [1ry8_B]
  • SWISS-PROT database: [P42330]
  • Domain organization of [AK1C3_HUMAN] by SWISSPFAM
  • Other resources with information on 1RY8
  • Community annotation for 1RY8 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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