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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  KNOWLEDGE BASED MODEL OF THE MEMBRANE PROTEIN, CYCLOOXYGENASE (COX-1) AND NSAID COMPLEX
 
Authors :  A. Banerjee, A. K. Pal, S. Bhattacharyya
Date :  03 Dec 99  (Deposition) - 17 Dec 99  (Release) - 17 Dec 99  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,_#
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Nsaid-Cox-1 Complex, Antiinflammatory, Antipyretic Agents, Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Banerjee, A. K. Pal, S. Chakraborty, S. Ghosh, S. Bhattacharyya
Structural Basis Of Antiinflammatory Activity Of N-Phenyl Dichloroacetanilide. A Knowledge Based Molecular Modelling Study Of Complex Of Cox-1 With N-Phenyl Dichloroacetanilide (Nsaid) Using The X-Ray Structure Of Cox-1-Aspirin Complex.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROSTAGLANDIN ENDOPEROXIDE SYNTHASE
    ChainsA
    EC Number1.14.99.1
    OrganelleSEMINAL VESICLE
    Organism CommonSHEEP
    Organism ScientificOVIS ARIES
    SecretionSEMEN
    SynonymCYCLOOXYGENASE

 Structural Features

(-) Chains, Units

  
Theoretical Model 
#:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Theoretical Model (4, 7)
No.NameCountTypeFull Name
1BOG1Ligand/IonB-OCTYLGLUCOSIDE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NSA1Ligand/Ion2,2-DICHLORO-N-PHENYL-ACETAMIDE

(-) Sites  (0, 0)

(no "Site" information available for 1DJJ)

(-) SS Bonds  (5, 5)

Theoretical Model
No.Residues
1A:36 -A:47
2A:37 -A:159
3A:41 -A:57
4A:59 -A:69
5A:569 -A:575

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ser A:126 -Pro A:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Theoretical Model (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PGH1_SHEEP_001 *R97HPGH1_SHEEP  ---  ---AR97H
2UniProtVAR_PGH1_SHEEP_002 *D164GPGH1_SHEEP  ---  ---AG164G
3UniProtVAR_PGH1_SHEEP_003 *R456QPGH1_SHEEP  ---  ---AR456Q
4UniProtVAR_PGH1_SHEEP_004 *E520KPGH1_SHEEP  ---  ---AE520K
5UniProtVAR_PGH1_SHEEP_005 *E520QPGH1_SHEEP  ---  ---AE520Q
6UniProtVAR_PGH1_SHEEP_006 *M525IPGH1_SHEEP  ---  ---AM525I
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_3PS50292 Animal heme peroxidase superfamily profile.PGH1_SHEEP110-600  1A:110-583

(-) Exons   (0, 0)

(no "Exon" information available for 1DJJ)

(-) Sequences/Alignments

Theoretical Model
   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:551
 aligned with PGH1_SHEEP | P05979 from UniProtKB/Swiss-Prot  Length:600

    Alignment length:551
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582 
           PGH1_SHEEP    33 VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMDTKGKKQLPDAEFLSRRFLLRRKFIPDPQSTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVP 583
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.hhhhheeee.....eeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......ee.......hhhhhh....ee......................hhhhhhhhhh............hhhhhhhhhhhhh......................hhhhhh.hhhhhhhhh.........eee..eee.................hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhh...eee..eeehhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhh............. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------H------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------------------------------------------------------------K----I---------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------------------------------PEROXIDASE_3  PDB: A:110-583 UniProt: 110-600                                                                                                                                                                                                                                                                                                                                                                                                                                              PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1djj A  33 VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVP 583
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582 

   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  (0, 0)

(no "SCOP Domain" information available for 1DJJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1DJJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DJJ)

(-) Gene Ontology  (25, 25)

Theoretical Model(hide GO term definitions)
Chain A   (PGH1_SHEEP | P05979)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0004666    prostaglandin-endoperoxide synthase activity    Catalysis of the reaction: arachidonate + donor-H2 + 2 O2 = prostaglandin H2 + acceptor + H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
    GO:0006979    response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGH1_SHEEP | P059791cqe 1diy 1ebv 1eqg 1eqh 1fe2 1ht5 1ht8 1igx 1igz 1pge 1pgf 1pgg 1prh 1pth 1q4g 1u67 2ayl 2oye 2oyu 3kk6 3n8v 3n8w 3n8x 3n8y 3n8z 4o1z

(-) Related Entries Specified in the PDB File

1pth 1PTH CONTAINS THE SAME PROTEIN COMPLEXED WITH ASPIRIN