1V3T Oxidoreductase date Nov 05, 2003
title Crystal Structure Of Leukotriene B4 12- Hydroxydehydrogenase15-Oxo-Prostaglandin 13-Reductase
authors T.Hori, T.Yokomizo, H.Ago, M.Sugahara, G.Ueno, M.Yamamoto, T.Kumasaka, T.Shimizu, M.Miyano, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Leukotriene B4 12- Hydroxydehydrogenaseprostaglandin 15-Keto Reductase;
Chain: A, B
Synonym: Leukotriene B4 12-Hydroxydehydrogenase15-Oxo- Prostaglandin 13-Reductase;
Ec: 1.3.1.48
Engineered: Yes
Organism_scientific: Cavia Porcellus
Organism_common: Domestic Guinea Pig
Organism_taxid: 10141
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex
symmetry Space Group: P 1 21 1
R_factor 0.194 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.748 77.071 79.601 90.00 102.73 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand NAP enzyme Oxidoreductase E.C.1.3.1.48 BRENDA
related structures by homologous chain: 1V3U, 1ZSV
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop., Hori T, Yokomizo T, Ago H, Sugahara M, Ueno G, Yamamoto M, Kumasaka T, Shimizu T, Miyano M, J Biol Chem 2004 May 21;279(21):22615-23. Epub 2004 Mar 8. PMID:15007077
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (1v3t.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 1V3T
  • CSU: Contacts of Structural Units for 1V3T
  • Likely Quarternary Molecular Structure file(s) for 1V3T
  • Structure Factors (228 Kb)
  • Retrieve 1V3T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V3T from S2C, [Save to disk]
  • Re-refined 1v3t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V3T 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 1V3T
  • 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 1V3T, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v3ta1, region A:1-112,A:295-329 [Jmol] [rasmolscript] [script source]
        - Domain d1v3ta2, region A:113-294 [Jmol] [rasmolscript] [script source]
        - Domain d1v3tb1, region B:1-112,B:295-329 [Jmol] [rasmolscript] [script source]
        - Domain d1v3tb2, region B:113-294 [Jmol] [rasmolscript] [script source]
  • Fold representative 1v3t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1v3t_A] [1v3t] [1v3t_B]
  • SWISS-PROT database: [Q9EQZ5]
  • Domain organization of [PTGR1_CAVPO] by SWISSPFAM
  • Other resources with information on 1V3T
  • Community annotation for 1V3T 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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