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(-) Description

Title :  INDOMETHACIN-(S)-ALPHA-ETHYL-ETHANOLAMIDE BOUND TO CYCLOOXYGENASE-1
 
Authors :  C. A. Harman, R. M. Garavito
Date :  23 Feb 07  (Deposition) - 24 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  P
Biol. Unit 1:  P  (2x)
Keywords :  Cox, Pghs, Indomethacin, Nsaid, Heme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Harman, M. V. Turman, K. R. Kozak, L. J. Marnett, W. L. Smith, R. M. Garavito
Structural Basis Of Enantioselective Inhibition Of Cyclooxygenase-1 By S-Alpha-Substituted Indomethacin Ethanolamides.
J. Biol. Chem. V. 282 28096 2007
PubMed-ID: 17656360  |  Reference-DOI: 10.1074/JBC.M701335200

(-) Compounds

Molecule 1 - PROSTAGLANDIN G/H SYNTHASE 1
    ChainsP
    EC Number1.14.99.1
    Organism CommonSHEEP
    Organism ScientificOVIS ARIES
    Organism Taxid9940
    Other DetailsSHEEP VESICULAR GLAND
    SynonymCYCLOOXYGENASE-1, COX-1, PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 1, PROSTAGLANDIN H2 SYNTHASE 1, PGH SYNTHASE 1, PGHS-1, PHS 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit P
Biological Unit 1 (2x)P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric Unit (5, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2BOG2Ligand/IonB-OCTYLGLUCOSIDE
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IMS1Ligand/Ion2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL-1H-INDOL-3-YL]-N-[(1S)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (5, 22)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2BOG4Ligand/IonB-OCTYLGLUCOSIDE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IMS2Ligand/Ion2-[1-(4-CHLOROBENZOYL)-5-METHOXY-2-METHYL-1H-INDOL-3-YL]-N-[(1S)-1-(HYDROXYMETHYL)PROPYL]ACETAMIDE
5NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR P:55 , ASN P:68 , NAG P:662BINDING SITE FOR RESIDUE NAG P 661
02AC2SOFTWARETYR P:38 , NAG P:661BINDING SITE FOR RESIDUE NAG P 662
03AC3SOFTWAREGLU P:140 , ASN P:144 , TYR P:147 , LEU P:238 , NAG P:672 , HOH P:759BINDING SITE FOR RESIDUE NAG P 671
04AC4SOFTWAREMET P:216 , GLU P:239 , NAG P:671 , BMA P:673 , HOH P:789BINDING SITE FOR RESIDUE NAG P 672
05AC5SOFTWARENAG P:672BINDING SITE FOR RESIDUE BMA P 673
06AC6SOFTWAREGLY P:278 , PRO P:280 , TYR P:402 , GLN P:406 , ASN P:410 , NAG P:682BINDING SITE FOR RESIDUE NAG P 681
07AC7SOFTWARETYR P:402 , GLN P:406 , NAG P:681BINDING SITE FOR RESIDUE NAG P 682
08AC8SOFTWARESER P:87 , PHE P:88BINDING SITE FOR RESIDUE BOG P 750
09AC9SOFTWAREPRO P:86 , ILE P:89 , VAL P:119 , ARG P:120 , LEU P:123 , GLU P:524BINDING SITE FOR RESIDUE BOG P 751
10BC1SOFTWAREHIS P:90 , MET P:113 , VAL P:116 , ARG P:120 , GLN P:192 , VAL P:349 , LEU P:352 , SER P:353 , TYR P:355 , LEU P:359 , TRP P:387 , SER P:516 , PHE P:518 , ILE P:523 , GLY P:526 , ALA P:527 , SER P:530 , LEU P:531BINDING SITE FOR RESIDUE IMS P 700
11BC2SOFTWAREALA P:199 , ALA P:202 , GLN P:203 , THR P:206 , HIS P:207 , PHE P:210 , LYS P:211 , THR P:212 , LEU P:295 , ASN P:382 , HIS P:386 , TRP P:387 , HIS P:388 , MET P:391 , VAL P:447 , ASP P:450 , HOH P:763BINDING SITE FOR RESIDUE HEM P 601

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1P:36 -P:47
2P:37 -P:159
3P:41 -P:57
4P:59 -P:69
5P:569 -P:575

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser P:126 -Pro P:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PGH1_SHEEP_001 *R97HPGH1_SHEEP  ---  ---PR97H
2UniProtVAR_PGH1_SHEEP_002 *D164GPGH1_SHEEP  ---  ---PG164G
3UniProtVAR_PGH1_SHEEP_003 *R456QPGH1_SHEEP  ---  ---PR456Q
4UniProtVAR_PGH1_SHEEP_004 *E520KPGH1_SHEEP  ---  ---PE520K
5UniProtVAR_PGH1_SHEEP_005 *E520QPGH1_SHEEP  ---  ---PE520Q
6UniProtVAR_PGH1_SHEEP_006 *M525IPGH1_SHEEP  ---  ---PM525I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PGH1_SHEEP_001 *R97HPGH1_SHEEP  ---  ---PR97H
2UniProtVAR_PGH1_SHEEP_002 *D164GPGH1_SHEEP  ---  ---PG164G
3UniProtVAR_PGH1_SHEEP_003 *R456QPGH1_SHEEP  ---  ---PR456Q
4UniProtVAR_PGH1_SHEEP_004 *E520KPGH1_SHEEP  ---  ---PE520K
5UniProtVAR_PGH1_SHEEP_005 *E520QPGH1_SHEEP  ---  ---PE520Q
6UniProtVAR_PGH1_SHEEP_006 *M525IPGH1_SHEEP  ---  ---PM525I
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.PGH1_SHEEP32-70  1P:32-70
2PEROXIDASE_3PS50292 Animal heme peroxidase superfamily profile.PGH1_SHEEP110-600  1P:110-584
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.PGH1_SHEEP32-70  2P:32-70
2PEROXIDASE_3PS50292 Animal heme peroxidase superfamily profile.PGH1_SHEEP110-600  2P:110-584

(-) Exons   (0, 0)

(no "Exon" information available for 2OYU)

(-) 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 P from PDB  Type:PROTEIN  Length:553
 aligned with PGH1_SHEEP | P05979 from UniProtKB/Swiss-Prot  Length:600

    Alignment length:553
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581   
           PGH1_SHEEP    32 PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMDTKGKKQLPDAEFLSRRFLLRRKFIPDPQSTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVPD 584
               SCOP domains d2oyup2 P:32-73 automated matches         d2oyup1 P:74-584 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -2oyuP01 P:33-73 Laminin                  2oyuP02 P:74-583 Myeloperoxidase, subunit C                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------An_peroxidase-2oyuP01 P:142-582                                                                                                                                                                                                                                                                                                                                                                                                                          -- Pfam domains
         Sec.struct. author ..hhhhhh......eeeee...eeeee.....ee.....eehhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhh............................hhhhhhhhhh............hhhhhhhhhhhhh.............................hhhhhhhhh.........eee..eee................................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...........hhhhhhhhhhhhhh...eee..eeehhhhhh...hhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhh.............. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------------------------------H------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------------------------------------------------------------K----I----------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q---------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE EGF_3  PDB: P:32-70 UniProt: 32-70     ---------------------------------------PEROXIDASE_3  PDB: P:110-584 UniProt: 110-600                                                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oyu P  32 PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFLLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVPD 584
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain P   (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 1djj 1ebv 1eqg 1eqh 1fe2 1ht5 1ht8 1igx 1igz 1pge 1pgf 1pgg 1prh 1pth 1q4g 1u67 2ayl 2oye 3kk6 3n8v 3n8w 3n8x 3n8y 3n8z 4o1z

(-) Related Entries Specified in the PDB File

1cqe FLURIBPROFEN BOUND TO COX-1
1eqe FLURBIPROFEN BOUND TO COX-1 (HIGHER RESOLUTION)
1pgf INDOMETHACIN BOUND TO COX-1
1pgg INDOMETHACIN BOUND TO COX-1 (TRANS MODEL)
2oye