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(-) Description

Title :  STRUCTURE-FUNCTION ANALYSIS OF HUMAN L-PROSTAGLANDIN D SYNTHASE BOUND WITH FATTY ACID
 
Authors :  Y. Zhou, N. Shaw, Y. Li, Y. Zhao, R. Zhang, Z. -J. Liu
Date :  22 Jul 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipocalin, Prostaglandin Synthase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Zhou, N. Shaw, Y. Li, Y. Zhao, R. Zhang, Z. -J. Liu
Structure-Function Analysis Of Human L-Prostaglandin D Synthase Bound With Fatty Acid
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROSTAGLANDIN-H2 D-ISOMERASE
    ChainsA
    EC Number5.3.99.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 29-190
    GenePTGDS, PDS
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE, GLUTATHIONE- INDEPENDENT PGD SYNTHASE, PROSTAGLANDIN-D2 SYNTHASE, PGD2 SYNTHASE, PGDS2, PGDS, BETA-TRACE PROTEIN, CEREBRIN-28

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1OLA2Ligand/IonOLEIC ACID
2PLM2Ligand/IonPALMITIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:55 , LYS A:59 , LEU A:62 , SER A:81 , PHE A:83 , ARG A:92 , MET A:145 , PLM A:192 , PLM A:201 , HOH A:287BINDING SITE FOR RESIDUE OLA A 200
2AC2SOFTWAREASN A:51 , SER A:52 , LEU A:55 , MET A:94 , TYR A:116 , SER A:133 , ASP A:142 , PHE A:143 , MET A:145 , OLA A:191 , PLM A:192 , OLA A:200BINDING SITE FOR RESIDUE PLM A 201
3AC3SOFTWARELEU A:48 , LEU A:55 , LYS A:59 , LEU A:62 , MET A:64 , SER A:81 , THR A:147 , TYR A:149 , LEU A:180 , PLM A:192 , HOH A:194 , PLM A:201 , HOH A:287BINDING SITE FOR RESIDUE OLA A 191
4AC4SOFTWAREMET A:94 , TYR A:116 , VAL A:118 , SER A:133 , PRO A:139 , ASP A:142 , MET A:145 , OLA A:191 , OLA A:200 , PLM A:201 , HOH A:287 , HOH A:338BINDING SITE FOR RESIDUE PLM A 192

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:89 -A:186

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O22)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_004273R56QPTGDS_HUMANPolymorphism11552179AR56Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.PTGDS_HUMAN33-46  1A:33-46

(-) Exons   (0, 0)

(no "Exon" information available for 3O22)

(-) 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:157
 aligned with PTGDS_HUMAN | P41222 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:160
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
          PTGDS_HUMAN    29 SVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVVAPATDGGLNLTSTFLRKNQCETRTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGPGEDFRMATLYSRTQTPRAELKEKFTAFCKAQGFTEDTIVFLPQTDKCMT 188
               SCOP domains d3o22a_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Lipocalin-3o22A01 A:40-184                                                                                                                       ---- Pfam domains
         Sec.struct. author ......hhhhhheeeeeeeeee.hhhhhhhhhh.eeeeeeeee.....eeeeeeeee..eeeeeeeeeee.....eeeee..---.eeeeeeeee....eeeeeeeeeehhhhh.eeeeeee.....hhhhhhhhhhhhhhh..hhh.eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------Q------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----LIPOCALIN     ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o22 A  29 SVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMAKSVVAPATDGGLNLTSTFLRKNQCETRTMLLQPAGSLGSYSYRSP---STYSVSVVETDYDQYALLYSQGSKGPGEDFRMATLYSRTQTPRAELKEKFTAFCKAQGFTEDTIVFLPQTDKCMT 188
                                    38        48        58        68        78        88        98       108 |   | 118       128       138       148       158       168       178       188
                                                                                                           110 114                                                                          

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O22)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PTGDS_HUMAN | P41222)
molecular function
    GO:0005504    fatty acid binding    Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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: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:0005501    retinoid binding    Interacting selectively and non-covalently with retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
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: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: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:0045187    regulation of circadian sleep/wake cycle, sleep    Any process that modulates the frequency, rate or extent of sleep; a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005791    rough endoplasmic reticulum    The rough (or granular) endoplasmic reticulum (ER) has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTGDS_HUMAN | P412222wwp 3o19 3o2y 4imn 4imo 4orr 4ors 4oru 4orw 4orx 4ory 4os0 4os3 4os8 5wy9

(-) Related Entries Specified in the PDB File

3o19 3o2y