2VD1 Isomerase date Sep 28, 2007
title Complex Structure Of Prostaglandin D2 Synthase At 2.25a.
authors M.Hohwy, L.Spadola, B.Lundquist, K.Von Wachenfeldt, S.Persdotter P.Hawtin, J.Dahmen, I.Groth-Clausen, R.H.A.Folmer, K.Edman
compound source
Molecule: Glutathione-Requiring Prostaglandin D Synthase
Chain: A, B, C, D
Synonym: Glutathione-Dependent Pgd Synthetase, Prostaglandi Isomerase, Hematopoietic Prostaglandin D Synthase, H-Pgds, Prostaglandin D2 Synthase;
Ec: 5.3.99.2
Engineered: Yes
Other_details: The Protein Contain A Glutathione Co-Factor.
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: I 41
R_factor 0.184 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.521 123.521 106.289 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand D28, GSH, MG BindingDB enzyme Isomerase E.C.5.3.99.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceNovel prostaglandin d synthase inhibitors generated by fragment-based drug design., Hohwy M, Spadola L, Lundquist B, Hawtin P, Dahmen J, Groth-Clausen I, Nilsson E, Persdotter S, von Wachenfeldt K, Folmer RH, Edman K, J Med Chem. 2008 Apr 10;51(7):2178-86. Epub 2008 Mar 15. PMID:18341273
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (2vd1.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (2vd1.pdb2.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 2VD1
  • CSU: Contacts of Structural Units for 2VD1
  • Likely Quarternary Molecular Structure file(s) for 2VD1
  • Structure Factors (303 Kb)
  • Retrieve 2VD1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VD1 from S2C, [Save to disk]
  • Re-refined 2vd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VD1 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 2VD1
  • 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 2VD1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u2vd1, region D:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1t2vd1, region D:1647-1757 [Jmol] [rasmolscript] [script source]
        - Domain d1a2vd1, region D:237-672 [Jmol] [rasmolscript] [script source]
        - Domain d1q2vd1, region D:9-145,D:406-526 [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vd1_B] [2vd1_C] [2vd1] [2vd1_A] [2vd1_D]
  • SWISS-PROT database: [O60760]
  • Domain organization of [HPGDS_HUMAN] by SWISSPFAM
  • Other resources with information on 2VD1
  • Community annotation for 2VD1 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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