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(-) Description

Title :  HIGH QUALITY STRUCTURE OF CLEAVED PAI-1-STAB
 
Authors :  M. Dewilde, P. J. Declerck, A. Rabijns, S. V. Strelkov
Date :  29 Sep 08  (Deposition) - 17 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Cleaved Plasminogen Activator Inhibitor-1, Pai-1, Serpin, Stabilized, Glycoprotein, Plasminogen Activation, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Dewilde, S. V. Strelkov, A. Rabijns, P. J. Declerck
High Quality Structure Of Cleaved Pai-1-Stab.
J. Struct. Biol. V. 165 126 2009
PubMed-ID: 19059484  |  Reference-DOI: 10.1016/J.JSB.2008.11.001

(-) Compounds

Molecule 1 - PLASMINOGEN ACTIVATOR INHIBITOR 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPIGE20
    Expression System StrainMC1061
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPAI-1
    GeneSERPINE1, PAI1, PLANH1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPAI-1, PAI, ENDOTHELIAL PLASMINOGEN ACTIVATOR INHIBITOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EOX)

(-) Sites  (0, 0)

(no "Site" information available for 3EOX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EOX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:172 -Gly A:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013086H25PPAI1_HUMANPolymorphism2227647AH2P
2UniProtVAR_013087R209HPAI1_HUMANPolymorphism2227669AR186H
3UniProtVAR_013088T255NPAI1_HUMANPolymorphism2227685AT232N

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.PAI1_HUMAN375-385  1A:352-362

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002230951aENSE00001714420chr7:100770370-100770525156PAI1_HUMAN-00--
1.2bENST000002230952bENSE00000881563chr7:100771674-100771945272PAI1_HUMAN1-91911A:1-6868
1.3bENST000002230953bENSE00000712140chr7:100773702-100773935234PAI1_HUMAN91-169791A:68-146 (gaps)79
1.4ENST000002230954ENSE00000712144chr7:100775156-100775350195PAI1_HUMAN169-234661A:146-21166
1.5aENST000002230955aENSE00000712149chr7:100776976-100777174199PAI1_HUMAN234-300671A:211-27767
1.6ENST000002230956ENSE00000712153chr7:100778775-100778875101PAI1_HUMAN300-334351A:277-31135
1.7ENST000002230957ENSE00000712158chr7:100778996-10077908287PAI1_HUMAN334-363301A:311-34030
1.8ENST000002230958ENSE00000712164chr7:100780282-10078036584PAI1_HUMAN363-391291A:340-368 (gaps)29
1.9aENST000002230959aENSE00001055519chr7:100780686-1007825471862PAI1_HUMAN391-402121A:368-37912

(-) 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:370
 aligned with PAI1_HUMAN | P05121 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:379
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393         
           PAI1_HUMAN    24 VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISNLLGKGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVAQALQKVKIEVNESGTVASSSTAVIVSARMAPEEIIMDRPFLFVVRHNPTGTVLFMGQVMEP 402
               SCOP domains d3eoxa_ A: Plasminogen activator inhibitor-1                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------3eoxA01 A:33-170,A:281-325,A:343-360 Antithrombin, subunit I, domain 2                                                                    3eoxA02 A:171-280,A:326-342 Alpha-1-antitrypsin, domain 1                                                     3eoxA01 A:33-170,A:281-325,A:343-360         3eoxA02          3       eoxA01    ------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.......hhhhhhhh..--..eee...hhhhhhhhhhhhhhhh...................eeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee......hhhhhh..hhhhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh..................eeeeeeeeee...eeeeeeeeeee.-------.ee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -P---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------H---------------------------------------------N--------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-68 UniProt: 1-91 [INCOMPLETE]                   -----------------------------------------------------------------------------Exon 1.4  PDB: A:146-211 UniProt: 169-234                         -----------------------------------------------------------------Exon 1.6  PDB: A:277-311           ----------------------------Exon 1.8 UniProt: 363-391    ----------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.3b  PDB: A:68-146 (gaps) UniProt: 91-169                                ----------------------------------------------------------------Exon 1.5a  PDB: A:211-277 UniProt: 234-300                         ---------------------------------Exon 1.7  PDB: A:311-340      ---------------------------Exon 1.9a    Transcript 1 (2)
                 3eox A   1 VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLF--TVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRPFQADFTSLSDQEPLHVALALQKVKIEVNESGTVASSSTAVIV-------EIIIDRPFLFVVRHNPTGTVLFMGQVMEP 379
                                    10        20        30        40        50        60        70        80        90       100       110      |120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  |      -|      360       370         
                                                                                                                                              117  |                                                                                                                                                                                                                            343     351                            
                                                                                                                                                 120                                                                                                                                                                                                                                                                   

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EOX)

(-) Gene Ontology  (41, 41)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAI1_HUMAN | P05121)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0001300    chronological cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0033629    negative regulation of cell adhesion mediated by integrin    Any process that stops, prevents, or reduces the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:2000352    negative regulation of endothelial cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0051918    negative regulation of fibrinolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0010757    negative regulation of plasminogen activation    Any process that decreases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
    GO:0014912    negative regulation of smooth muscle cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell migration.
    GO:2000098    negative regulation of smooth muscle cell-matrix adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell-matrix adhesion.
    GO:0061044    negative regulation of vascular wound healing    Any process that decreases the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature.
    GO:0061045    negative regulation of wound healing    Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0030194    positive regulation of blood coagulation    Any process that activates or increases the frequency, rate or extent of blood coagulation.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0032757    positive regulation of interleukin-8 production    Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
    GO:0035491    positive regulation of leukotriene production involved in inflammatory response    Any process that increases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response.
    GO:0090026    positive regulation of monocyte chemotaxis    Any process that increases the frequency, rate, or extent of monocyte chemotaxis.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0010469    regulation of receptor activity    Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
cellular component
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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    Asn A:172 - Gly A:173   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAI1_HUMAN | P051211a7c 1b3k 1c5g 1db2 1dvm 1dvn 1lj5 1oc0 3cvm 3pb1 3q02 3q03 3r4l 3ut3 4aqh 4g8o 4g8r 4ic0 5brr 9pai

(-) Related Entries Specified in the PDB File

1db2 STABILIZED, INTACT, ACTIVE CONFORMATION OF PAI-1
9pai CLEAVED SUBSTRATE VARIANT OF PAI-1