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(-) Description

Title :  HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETIONMUTANT] COMPLEXED WITH PEPTIDE MIMICKING THE REACTIVE CENTER LOOP
 
Authors :  L. Jankova, S. J. Harrop, D. N. Saunders, J. L. Andrews, K. C. Bertram, A. R. Gould, M. S. Baker, P. M. G. Curmi
Date :  15 Aug 01  (Deposition) - 26 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,P
Keywords :  Serpin, Peptide Binding, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Jankova, S. J. Harrop, D. N. Saunders, J. L. Andrews, K. C. Bertram, A. R. Gould, M. S. Baker, P. M. G. Curmi
Crystal Structure Of The Complex Of Plasminogen Activator Inhibitor 2 With A Peptide Mimicking The Reactive Center Loop
J. Biol. Chem. V. 276 43374 2001
PubMed-ID: 11546761  |  Reference-DOI: 10.1074/JBC.M103021200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMINOGEN ACTIVATOR INHIBITOR-2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PLASMINOGEN ACTIVATOR INHIBITOR-2
    Chains: P
    Engineered: YES
    Fragment: RESIDUES 367-380
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2BME1Ligand/IonBETA-MERCAPTOETHANOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:160 , CYS A:161 , GLU A:164BINDING SITE FOR RESIDUE BME A 561

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:405

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JRR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011743N120DPAI2_HUMANPolymorphism6098AN120D
2UniProtVAR_014173R229HPAI2_HUMANPolymorphism6100AR229H
3UniProtVAR_051946G374APAI2_HUMANPolymorphism34066931PG374A
4UniProtVAR_011744N404KPAI2_HUMANPolymorphism6103AN404K
5UniProtVAR_011745S413CPAI2_HUMANPolymorphism6104AS413C
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.PAI2_HUMAN388-398  1A:388-398

(-) Exons   (7, 8)

Asymmetric/Biological Unit (7, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002995022aENSE00001913834chr18:61554934-6155500471PAI2_HUMAN-00--
1.5ENST000002995025ENSE00001743384chr18:61558670-61558846177PAI2_HUMAN1-56561A:2-56
-		55
-
1.7ENST000002995027ENSE00001591590chr18:61562498-61562617120PAI2_HUMAN57-96401A:57-61
-		5
-
1.8cENST000002995028cENSE00001102622chr18:61564325-61564453129PAI2_HUMAN97-139431A:102-139
-		38
-
1.9bENST000002995029bENSE00002141382chr18:61564961-61565078118PAI2_HUMAN140-179401A:140-179
-		40
-
1.10ENST0000029950210ENSE00002158595chr18:61568974-61569116143PAI2_HUMAN179-226481A:179-226 (gaps)
-		48
-
1.11bENST0000029950211bENSE00002169488chr18:61569638-61569802165PAI2_HUMAN227-281551A:227-281 (gaps)
-		55
-
1.12bENST0000029950212bENSE00001812472chr18:61570135-61571124990PAI2_HUMAN282-4151342A:282-415 (gaps)
P:366-380		134
15

(-) 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:357
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:414
                                    11        21        31        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    
           PAI2_HUMAN     2 EDLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVGANAVTPMTPENFTSCGFMQQIQKGSYPDAILQAQAADKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
               SCOP domains d1jrra_ A: Plasminogen activator inhibitor-2                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1jrrA02 A:2-207,A:310-364 Antithrombin, subunit I, domain 2                                                                                                                                                   1jrrA01     A:208-309,A:385-411 Alpha-1-antitrypsin, domain 1                                         1jrrA02 A:2-207,A:310-364                              ---          -------1jrrA01 A:208-309,A:385-411---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh...----------------------------------------hhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh................eeeeeeeeeeeee......ee.----.eeeee..eeee..eeeeeeeeeeeeehhh.eeeeeee....eeeeeeee.---.....hhhhhhhhhhhhhhhhhh....eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh..............eeeeeeeeeeeeee.....----------.........eee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------C-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:2-56 UniProt: 1-56 [INCOMPLETE]       Exon 1.7  PDB: A:57-61 UniProt: 57-96   Exon 1.8c  PDB: A:102-139 UniProt: 97-139  ---------------------------------------Exon 1.10  PDB: A:179-226 (gaps)                Exon 1.11b  PDB: A:227-281 (gaps) UniProt: 227-281     Exon 1.12b  PDB: A:282-415 (gaps) UniProt: 282-415                                                                                     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:140-179               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1jrr A   2 EDLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFN----------------------------------------KIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKK----YPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPD---DVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGT----------TGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
                                    11        21        31        41        51        61         -         -         -         -|      111       121       131       141       151       161       171       181       191       201       211   |   221       231       241       251       261        |-  |    281       291       301       311       321       331       341       351       361     |   -      |381       391       401       411    
                                                                                      61                                      102                                                                                                              215  220                                               270 274                                                                                          367        378                                     


Chain P from PDB  Type:PROTEIN  Length:15
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:15
                                   375     
           PAI2_HUMAN   366 GTEAAAGTGGVMTGR 380
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
           Pfam domains (1) -Serpin-1jrrP01 Pfam domains (1)
           Pfam domains (2) -Serpin-1jrrP02 Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------A------ SAPs(SNPs)
                    PROSITE --------------- PROSITE
           Transcript 1 (1) Exon 1.12b      Transcript 1 (1)
           Transcript 1 (2) --------------- Transcript 1 (2)
                 1jrr P 366 xTEAAAGTGGVMTGR 380
                            |      375     
                          366-ACE
   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
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Serpin] (63)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,P   (PAI2_HUMAN | P05120)
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: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:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic 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: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:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAI2_HUMAN | P05120: 1by7 2arq 2arr

(-) Related Entries Specified in the PDB File

1by7 1BY7 CONTAINS HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT