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(-) Description

Title :  CRYSTAL STRUCTURE OF HH-PGDS WITH WATER DISPLACING INHIBITOR
 
Authors :  J. E. Day, A. Thorarensen, J. I. Trujillo
Date :  28 Mar 12  (Deposition) - 18 Jul 12  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor, Solvent Replacement, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  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
Investigation Of The Binding Pocket Of Human Hematopoietic Prostaglandin (Pg) D2 Synthase (Hh-Pgds): A Tale Of Two Waters.
Bioorg. Med. Chem. Lett. V. 22 3795 2012
PubMed-ID: 22546671  |  Reference-DOI: 10.1016/J.BMCL.2012.04.004

(-) Compounds

Molecule 1 - HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
    Chains: A, B
    EC Number: 5.3.99.2, 2.5.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GSTS, HPGDS, PGDS, PTGDS2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H-PGDS, GST CLASS-SIGMA, GLUTATHIONE S-TRANSFERASE, GLUTATHIONE-DEPENDENT PGD SYNTHASE, GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE, PROSTAGLANDIN-H2 D-ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
10O42Ligand/Ion4-(ISOQUINOLIN-1-YL)-N-[2-(MORPHOLIN-4-YL)ETHYL]BENZAMIDE
2GSF2Ligand/IonL-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:318 , HOH A:323 , HOH A:334 , HOH B:317 , HOH B:349 , HOH B:356BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREMET A:11 , GLY A:13 , ARG A:14 , ASP A:96 , MET A:99 , TRP A:104 , TYR A:152 , LEU A:199 , GSF A:203 , HOH A:320BINDING SITE FOR RESIDUE 0O4 A 202
3AC3SOFTWARETYR A:8 , PHE A:9 , ARG A:14 , LYS A:43 , GLY A:49 , LYS A:50 , ILE A:51 , PRO A:52 , GLN A:63 , SER A:64 , 0O4 A:202 , HOH A:326 , HOH A:327 , HOH A:355 , HOH A:357 , HOH A:398 , ASP B:97BINDING SITE FOR RESIDUE GSF A 203
4AC4SOFTWAREPHE B:9 , MET B:11 , GLY B:13 , ARG B:14 , ASP B:96 , MET B:99 , SER B:100 , TRP B:104 , TYR B:152 , GSF B:202 , HOH B:344 , HOH B:430 , HOH B:453BINDING SITE FOR RESIDUE 0O4 B 201
5AC5SOFTWAREASP A:97 , TYR B:8 , PHE B:9 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , GLN B:63 , SER B:64 , 0O4 B:201 , HOH B:318 , HOH B:321 , HOH B:322 , HOH B:325 , HOH B:427BINDING SITE FOR RESIDUE GSF B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EE0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ile A:34 -Glu A:35
2Ile A:51 -Pro A:52
3Ile B:51 -Pro B:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EE0)

(-) Exons   (0, 0)

(no "Exon" information available for 4EE0)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains d4ee0a1 A:2-75 automated matches                                      d4ee0a2 A:76-199 automated matches                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeeee..hhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ee0 A   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31   ||   45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    
                                                            35|                                                                                                                                                               
                                                             40                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains d4ee0b1 B:1-75 automated matches                                         d4ee0b2 B:76-199 automated matches                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhh...eeeee.hhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ee0 B   1 HPNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    10        20        30   ||   42        52        62        72        82        92       102   ||  114       124       134       144       154       164       174       184       194     
                                                            34|                                                                  106|                                                                                          
                                                             37                                                                   109
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EE0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EE0)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile A:34 - Glu A:35   [ RasMol ]  
    Ile A:51 - Pro A:52   [ RasMol ]  
    Ile B:51 - Pro B:52   [ RasMol ]  
 

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  4ee0
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HPGDS_HUMAN | O60760: 1iyh 1iyi 1v40 2cvd 2vcq 2vcw 2vcx 2vcz 2vd0 2vd1 3ee2 3kxo 3vi5 3vi7 4ec0 4edy 4edz 5ais 5aiv 5aix

(-) Related Entries Specified in the PDB File

4edy 4edz