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PDBsum entry 4edz

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protein ligands metals Protein-protein interface(s) links
Isomerase/isomerase inhibitor PDB id
4edz
Jmol
Contents
Protein chain
198 a.a.
Ligands
GSH ×4
0O5 ×4
Metals
_MG ×2
Waters ×468
PDB id:
4edz
Name: Isomerase/isomerase inhibitor
Title: Crystal structure of hh-pgds with water displacing inhibitor
Structure: Hematopoietic prostaglandin d synthase. Chain: a, b, c, d. Synonym: h-pgds, gst class-sigma, glutathione s-transferase glutathione-dependent pgd synthase, glutathione-requiring prostaglandin d synthase, prostaglandin-h2 d-isomerase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gsts, hpgds, pgds, ptgds2. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.00Å     R-factor:   0.192     R-free:   0.236
Authors: J.E.Day,A.Thorarensen,J.I.Trujillo
Key ref: J.I.Trujillo et al. (2012). Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters. Bioorg Med Chem Lett, 22, 3795-3799. PubMed id: 22546671 DOI: 10.1016/j.bmcl.2012.04.004
Date:
27-Mar-12     Release date:   16-May-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O60760  (HPGDS_HUMAN) -  Hematopoietic prostaglandin D synthase
Seq:
Struc:
199 a.a.
198 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.2.5.1.18  - Glutathione transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RX + glutathione = HX + R-S-glutathione
RX
+
glutathione
Bound ligand (Het Group name = GSH)
corresponds exactly
= HX
+ R-S-glutathione
   Enzyme class 3: E.C.5.3.99.2  - Prostaglandin-D synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
(5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15-hydroxyprosta-5,13-dienoate
=
(5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
Bound ligand (Het Group name = 0O5)
matches with 43.24% similarity
      Cofactor: Glutathione
Glutathione
Bound ligand (Het Group name = GSH) corresponds exactly
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     small molecule metabolic process   12 terms 
  Biochemical function     transferase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.bmcl.2012.04.004 Bioorg Med Chem Lett 22:3795-3799 (2012)
PubMed id: 22546671  
 
 
Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters.
J.I.Trujillo, J.R.Kiefer, W.Huang, J.E.Day, J.Moon, G.M.Jerome, C.P.Bono, C.M.Kornmeier, M.L.Williams, C.Kuhn, G.R.Rennie, T.A.Wynn, C.P.Carron, A.Thorarensen.
 
  ABSTRACT  
 
No abstract given.