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(-) Description

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
Date :  28 Sep 07  (Deposition) - 15 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Prostaglandin Biosynthesis, Fatty Acid Biosynthesis, Prostaglandin D2 Synthase, Pgds, Asthma, Cytoplasm, Isomerase, Lipid Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Hohwy, L. Spadola, B. Lundquist, P. Hawtin, J. Dahmen, I. Groth-Clausen, E. Nilsson, S. Persdotter, K. Von Wachenfeldt, R. H. A. Folmer, K. Edman
Novel Prostaglandin D Synthase Inhibitors Generated By Fragment-Based Drug Design.
J. Med. Chem. V. 51 2178 2008
PubMed-ID: 18341273  |  Reference-DOI: 10.1021/JM701509K

(-) Compounds

Molecule 1 - GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
    ChainsA, B, C, D
    EC Number5.3.99.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHE PROTEIN CONTAIN A GLUTATHIONE CO-FACTOR.
    SynonymGLUTATHIONE-DEPENDENT PGD SYNTHETASE, PROSTAGLANDIN-H2 D-ISOMERASE, HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE, H-PGDS, PROSTAGLANDIN D2 SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1D281Ligand/Ion4-{[4-(4-FLUORO-3-METHYLPHENYL)-1,3-THIAZOL-2-YL]AMINO}-2-HYDROXYBENZOIC ACID
2GSH4Ligand/IonGLUTATHIONE
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1D281Ligand/Ion4-{[4-(4-FLUORO-3-METHYLPHENYL)-1,3-THIAZOL-2-YL]AMINO}-2-HYDROXYBENZOIC ACID
2GSH2Ligand/IonGLUTATHIONE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1D28-1Ligand/Ion4-{[4-(4-FLUORO-3-METHYLPHENYL)-1,3-THIAZOL-2-YL]AMINO}-2-HYDROXYBENZOIC ACID
2GSH2Ligand/IonGLUTATHIONE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:9 , MET B:11 , GLY B:13 , ARG B:14 , GLN B:36 , ASP B:96 , MET B:99 , TRP B:104 , TYR B:152 , GSH B:1202 , HOH B:2104BINDING SITE FOR RESIDUE D28 B1200
2AC2SOFTWAREHOH A:2043 , HOH A:2046 , HOH A:2048 , HOH B:2056 , HOH B:2059 , HOH B:2061BINDING SITE FOR RESIDUE MG B1201
3AC3SOFTWARETYR A:8 , ARG A:14 , TRP A:39 , LYS A:43 , GLY A:49 , LYS A:50 , ILE A:51 , GLN A:63 , SER A:64 , HOH A:2023 , HOH A:2047 , ASP B:97BINDING SITE FOR RESIDUE GSH A1200
4AC4SOFTWAREASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , GLN B:63 , SER B:64 , D28 B:1200 , HOH B:2010 , HOH B:2060 , HOH B:2107BINDING SITE FOR RESIDUE GSH B1202
5AC5SOFTWARETYR C:8 , ARG C:14 , TRP C:39 , LYS C:43 , LYS C:50 , ILE C:51 , GLN C:63 , SER C:64 , HOH C:2085 , HOH C:2086 , HOH C:2087 , ASP D:97BINDING SITE FOR RESIDUE GSH C1200
6AC6SOFTWAREASP C:97 , TYR D:8 , ARG D:14 , TRP D:39 , LYS D:43 , GLY D:49 , LYS D:50 , ILE D:51 , PRO D:52 , GLN D:63 , SER D:64 , HOH D:2020 , HOH D:2038BINDING SITE FOR RESIDUE GSH D1200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VD1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:51 -Pro A:52
2Ile B:51 -Pro B:52
3Ile C:51 -Pro C:52
4Ile D:51 -Pro D:52

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VD1)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.HPGDS_HUMAN2-79
 
 
 
  4A:2-79
B:2-79
C:2-79
D:2-79
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.HPGDS_HUMAN81-199
 
 
 
  4A:81-199
B:81-199
C:81-199
D:81-199
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.HPGDS_HUMAN2-79
 
 
 
  2A:2-79
B:2-79
-
-
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.HPGDS_HUMAN81-199
 
 
 
  2A:81-199
B:81-199
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GST_NTERPS50404 Soluble glutathione S-transferase N-terminal domain profile.HPGDS_HUMAN2-79
 
 
 
  2-
-
C:2-79
D:2-79
2GST_CTERPS50405 Soluble glutathione S-transferase C-terminal domain profile.HPGDS_HUMAN81-199
 
 
 
  2-
-
C:81-199
D:81-199

(-) Exons   (5, 20)

Asymmetric Unit (5, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002952561aENSE00001428701chr4:95264027-9526394682HPGDS_HUMAN-00--
1.2aENST000002952562aENSE00002147371chr4:95255789-95255648142HPGDS_HUMAN1-45454A:2-45
B:2-45
C:2-45
D:2-45
44
44
44
44
1.3ENST000002952563ENSE00001238639chr4:95239116-9523902493HPGDS_HUMAN45-76324A:45-76
B:45-76
C:45-76
D:45-76
32
32
32
32
1.4ENST000002952564ENSE00001071670chr4:95229894-95229785110HPGDS_HUMAN76-112374A:76-112
B:76-112
C:76-101
D:76-112
37
37
26
37
1.6ENST000002952566ENSE00001071668chr4:95223395-9522329799HPGDS_HUMAN113-145334A:113-145
B:113-145
C:117-145
D:113-145
33
33
29
33
1.7ENST000002952567ENSE00001302624chr4:95220795-952196861110HPGDS_HUMAN146-199544A:146-199
B:146-199
C:146-199
D:146-199
54
54
54
54

(-) Sequences/Alignments

Asymmetric 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:198
 aligned with HPGDS_HUMAN | O60760 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
          HPGDS_HUMAN     2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
               SCOP domains d2vd1a2 A:2-75 automated matches                                          d2vd1a1 A:76-199 automated matches                                                                                           SCOP domains
               CATH domains 2vd1A01 A:2-75,A:184-199 Glutaredoxin                                     2vd1A02 A:76-183  [code=1.20.1050.10, no name defined]                                                      2vd1A01          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GST_NTER  PDB: A:2-79 UniProt: 2-79                                           -GST_CTER  PDB: A:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:2-45 UniProt: 1-45        ------------------------------Exon 1.4  PDB: A:76-112              Exon 1.6  PDB: A:113-145         Exon 1.7  PDB: A:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vd1 A   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with HPGDS_HUMAN | O60760 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
          HPGDS_HUMAN     2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
               SCOP domains d2vd1b2 B:2-75 automated matches                                          d2vd1b1 B:76-199 automated matches                                                                                           SCOP domains
               CATH domains 2vd1B01 B:2-75,B:184-199 Glutaredoxin                                     2vd1B02 B:76-183  [code=1.20.1050.10, no name defined]                                                      2vd1B01          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GST_NTER  PDB: B:2-79 UniProt: 2-79                                           -GST_CTER  PDB: B:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:2-45 UniProt: 1-45        ------------------------------Exon 1.4  PDB: B:76-112              Exon 1.6  PDB: B:113-145         Exon 1.7  PDB: B:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: B:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vd1 B   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with HPGDS_HUMAN | O60760 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
          HPGDS_HUMAN     2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
               SCOP domains d2vd1c2 C:2-75 automated matches                                          d2vd1c1 C:76-199 automated                matches                                                                            SCOP domains
               CATH domains 2vd1C01 C:2-75,C:184-199 Glutaredoxin                                     2vd1C02 C:76-183  [code=1.               20.1050.10, no name defined]                                       2vd1C01          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..---------------.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GST_NTER  PDB: C:2-79 UniProt: 2-79                                           -GST_CTER  PDB: C:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: C:2-45 UniProt: 1-45        ------------------------------Exon 1.4  PDB: C:76-101 [INCOMPLETE] Exon 1.6  PDB: C:117-145         Exon 1.7  PDB: C:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: C:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vd1 C   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSC---------------NELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101         -     | 121       131       141       151       161       171       181       191        
                                                                                                                             101             117                                                                                  

Chain D from PDB  Type:PROTEIN  Length:198
 aligned with HPGDS_HUMAN | O60760 from UniProtKB/Swiss-Prot  Length:199

    Alignment length:198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        
          HPGDS_HUMAN     2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
               SCOP domains d2vd1d2 D:2-75 automated matches                                          d2vd1d1 D:76-199 automated matches                                                                                           SCOP domains
               CATH domains 2vd1D01 D:2-75,D:184-199 Glutaredoxin                                     2vd1D02 D:76-183  [code=1.20.1050.10, no name defined]                                                      2vd1D01          CATH domains
           Pfam domains (1) --GST_N-2vd1D05 D:4-73                                                  -------GST_C-2vd1D01 D:81-185                                                                                   -------------- Pfam domains (1)
           Pfam domains (2) --GST_N-2vd1D06 D:4-73                                                  -------GST_C-2vd1D02 D:81-185                                                                                   -------------- Pfam domains (2)
           Pfam domains (3) --GST_N-2vd1D07 D:4-73                                                  -------GST_C-2vd1D03 D:81-185                                                                                   -------------- Pfam domains (3)
           Pfam domains (4) --GST_N-2vd1D08 D:4-73                                                  -------GST_C-2vd1D04 D:81-185                                                                                   -------------- Pfam domains (4)
         Sec.struct. author ...eeeee.....hhhhhhhhhhh....eeeee...hhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE GST_NTER  PDB: D:2-79 UniProt: 2-79                                           -GST_CTER  PDB: D:81-199 UniProt: 81-199                                                                                 PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: D:2-45 UniProt: 1-45        ------------------------------Exon 1.4  PDB: D:76-112              Exon 1.6  PDB: D:113-145         Exon 1.7  PDB: D:146-199 UniProt: 146-199              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: D:45-76          --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2vd1 D   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        

   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, 8)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
1a2vd1A01A:2-75,A:184-199
1b2vd1B01B:2-75,B:184-199
1c2vd1C01C:2-75,C:184-199
1d2vd1D01D:2-75,D:184-199

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: GST_C (118)
(-)
Family: GST_C (102)
1aGST_C-2vd1D01D:81-185
1bGST_C-2vd1D02D:81-185
1cGST_C-2vd1D03D:81-185
1dGST_C-2vd1D04D:81-185

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HPGDS_HUMAN | O60760)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004364    glutathione transferase activity    Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004667    prostaglandin-D synthase activity    Catalysis of the reaction: prostaglandin H(2) = prostaglandin D(2).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0019371    cyclooxygenase pathway    The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:1901687    glutathione derivative biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione derivative.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:2000255    negative regulation of male germ cell proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation.
    GO:0001516    prostaglandin biosynthetic process    The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring.
    GO:0006693    prostaglandin metabolic process    The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric Unit
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 Related Entries

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

UniProtKB/Swiss-Prot
        HPGDS_HUMAN | O607601iyh 1iyi 1v40 2cvd 2vcq 2vcw 2vcx 2vcz 2vd0 3ee2 3kxo 3vi5 3vi7 4ec0 4edy 4edz 4ee0 5ais 5aiv 5aix

(-) Related Entries Specified in the PDB File

1iyh CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
1iyi CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
1v40 FIRST INHIBITOR COMPLEX STRUCTURE OF HUMAN HEMATOPOIETICPROSTAGLANDIN D SYNTHASE
2vcq COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
2vcw COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
2vcx COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.1A.
2vcz COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 1.95A.
2vd0 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.2A.