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(-) Description

Title :  CRYSTAL STRUCTURE OF ZEBRAFISH PLASMINOGEN ACTIVATOR INHIBITOR-1 (PAI-1)
 
Authors :  J. S. Johansen
Date :  21 Feb 12  (Deposition) - 27 Mar 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Active Serpin, Hydrolase Inhibitor, Zebarfish Upa (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Bager, J. S. Johansen, J. K. Jensen, A. Stensballe, A. Jendroszek, L. Buxbom, H. P. Sorensen, P. A. Andreasen
Protein Conformational Change Delayed By Steric Hindrance From An N-Linked Glycan.
J. Mol. Biol. V. 425 2867 2013
PubMed-ID: 23702291  |  Reference-DOI: 10.1016/J.JMB.2013.05.007

(-) Compounds

Molecule 1 - SERPIN PEPTIDASE INHIBITOR, CLADE E (NEXIN, PLASMINOGEN ACTIVATOR INHIBITOR TYPE 1), MEMBER 1
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cellular Location: KIDNEY
    Expression System Cell Line: HUMAN EMBRYONIC KIDNEY CELLS (HEK-293)
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: SERPINE1
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:183 , ASN A:185 , SER A:187BINDING SITE FOR RESIDUE NAG A 500
2AC2SOFTWAREASN B:185 , SER B:187 , GLN B:370 , GLN B:372BINDING SITE FOR RESIDUE NAG B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DTE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn B:185 -Gly B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DTE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DTE)

(-) Exons   (0, 0)

(no "Exon" information available for 4DTE)

(-) 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:374
 aligned with F1QRB8_DANRE | F1QRB8 from UniProtKB/TrEMBL  Length:392

    Alignment length:374
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388    
         F1QRB8_DANRE    19 NLIQDKQTDFGLQVFAEAVQSAPDRNLALSPYGIASVLGMAQMGAYGATLKLLASKMGYSLQERGMPKLQRLLQRDLASEDGVEVASGVMVDRKIILEKVFRRSLSKAFQSVPHQIDFSQPEMARQVINSWTSDHTDGMISEFLPSGVLSELTRLVFLNALHFHGVWKTPFDPRNTREQLFHTVNGSAVSVPMMTTTQKFNYGEFVSKDGVDYDVIEMPYEGESISMLLVTPFEKDVPLSALNKELSSSRIHQWRQEMRKISKQLSIPRFSMDTEIDLKSTLSRMGLGDIFSQSRADFSRITTEEPLCVSKVLQRVKLEVNEEGTKGSSATAAVIYSRMAVEEITLDRPFFFLIQHKPTGALLFSGQLTQPQEY 392
               SCOP domains d4dtea_ A: Plasminogen activator inhibitor-1                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhh...................eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh.hhhhhh..................eeeeeeeeee......................eee....eeeeeee.....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dte A   1 NLIQDKQTDFGLQVFAEAVQSAPDRNLALSPYGIASVLGMAQMGAYGATLKLLASKMGYSLQERGMPKLQRLLQRDLASEDGVEVASGVMVDRKIILEKVFRRSLSKAFQSVPHQIDFSQPEMARQVINSWTSDHTDGMISEFLPSGVLSELTRLVFLNALHFHGVWKTPFDPRNTREQLFHTVNGSAVSVPMMTTTQKFNYGEFVSKDGVDYDVIEMPYEGESISMLLVTPFEKDVPLSALNKELSSSRIHQWRQEMRKISKQLSIPRFSMDTEIDLKSTLSRMGLGDIFSQSRADFSRITTEEPLCVSKVLQRVKLEVNEEGTKGSSATAAVIYSRMAVEEITLDRPFFFLIQHKPTGALLFSGQLTQPQEY 374
                                    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       350       360       370    


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with F1QRB8_DANRE | F1QRB8 from UniProtKB/TrEMBL  Length:392

    Alignment length:372
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388  
         F1QRB8_DANRE    19 NLIQDKQTDFGLQVFAEAVQSAPDRNLALSPYGIASVLGMAQMGAYGATLKLLASKMGYSLQERGMPKLQRLLQRDLASEDGVEVASGVMVDRKIILEKVFRRSLSKAFQSVPHQIDFSQPEMARQVINSWTSDHTDGMISEFLPSGVLSELTRLVFLNALHFHGVWKTPFDPRNTREQLFHTVNGSAVSVPMMTTTQKFNYGEFVSKDGVDYDVIEMPYEGESISMLLVTPFEKDVPLSALNKELSSSRIHQWRQEMRKISKQLSIPRFSMDTEIDLKSTLSRMGLGDIFSQSRADFSRITTEEPLCVSKVLQRVKLEVNEEGTKGSSATAAVIYSRMAVEEITLDRPFFFLIQHKPTGALLFSGQLTQPQ 390
               SCOP domains d4dteb_ B: Plasminogen activator inhibitor-1                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh..................eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.....eeeeeeee.....hhhhhh...hhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh.hhhhhh..................eeeeeeeeee........--------.....eeee....eeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dte B   1 NLIQDKQTDFGLQVFAEAVQSAPDRNLALSPYGIASVLGMAQMGAYGATLKLLASKMGYSLQERGMPKLQRLLQRDLASEDGVEVASGVMVDRKIILEKVFRRSLSKAFQSVPHQIDFSQPEMARQVINSWTSDHTDGMISEFLPSGVLSELTRLVFLNALHFHGVWKTPFDPRNTREQLFHTVNGSAVSVPMMTTTQKFNYGEFVSKDGVDYDVIEMPYEGESISMLLVTPFEKDVPLSALNKELSSSRIHQWRQEMRKISKQLSIPRFSMDTEIDLKSTLSRMGLGDIFSQSRADFSRITTEEPLCVSKVLQRVKLEVNEEGTKGS--------SRMAVEEITLDRPFFFLIQHKPTGALLFSGQLTQPQ 372
                                    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       | -      |340       350       360       370  
                                                                                                                                                                                                                                                                                                                                                                 328      337
   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, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DTE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DTE)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (F1QRB8_DANRE | F1QRB8)
molecular 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: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: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.
cellular component
    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.

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