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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL SMALL MOLECULE INACTIVATOR BOUND TO PLASMINOGEN ACTIVATOR INHIBITOR-1
 
Authors :  J. A. Stuckey, D. A. Lawrence, S. -H. Li
Date :  23 Jul 12  (Deposition) - 25 Dec 13  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Serpin, Pai-1, Inhibitor, Blood Clotting, Blood Clotting-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Li, A. A. Reinke, K. L. Sanders, C. D. Emal, J. C. Whisstock, J. A. Stuckey, D. A. Lawrence
Mechanistic Characterization And Crystal Structure Of A Small Molecule Inactivator Bound To Plasminogen Activator Inhibitor-1.
Proc. Natl. Acad. Sci. Usa V. 110 E4941 2013
PubMed-ID: 24297881  |  Reference-DOI: 10.1073/PNAS.1216499110

(-) Compounds

Molecule 1 - PLASMINOGEN ACTIVATOR INHIBITOR 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: CRE/LOXP
    Fragment: UNP RESIDUES 28-402
    Gene: PAI-1, PAI1, PLANH1, SERPINE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAI, PAI-1, ENDOTHELIAL PLASMINOGEN ACTIVATOR INHIBITOR, SERPIN E1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
196P1Ligand/Ion(2S)-3-({[3-(TRIFLUOROMETHYL)PHENOXY]CARBONYL}AMINO)PROPANE-1,2-DIYL BIS(3,4,5-TRIHYDROXYBENZOATE)
2EDO1Ligand/Ion1,2-ETHANEDIOL
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
196P-1Ligand/Ion(2S)-3-({[3-(TRIFLUOROMETHYL)PHENOXY]CARBONYL}AMINO)PROPANE-1,2-DIYL BIS(3,4,5-TRIHYDROXYBENZOATE)
2EDO1Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
196P-1Ligand/Ion(2S)-3-({[3-(TRIFLUOROMETHYL)PHENOXY]CARBONYL}AMINO)PROPANE-1,2-DIYL BIS(3,4,5-TRIHYDROXYBENZOATE)
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
196P-1Ligand/Ion(2S)-3-({[3-(TRIFLUOROMETHYL)PHENOXY]CARBONYL}AMINO)PROPANE-1,2-DIYL BIS(3,4,5-TRIHYDROXYBENZOATE)
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
196P1Ligand/Ion(2S)-3-({[3-(TRIFLUOROMETHYL)PHENOXY]CARBONYL}AMINO)PROPANE-1,2-DIYL BIS(3,4,5-TRIHYDROXYBENZOATE)
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:149 , HIS A:150 , LYS A:323 , HOH A:517BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREASN A:31 , LEU A:280 , GLU A:281BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREILE B:148 , SER B:149 , HIS B:150 , GLU B:281 , LYS B:323BINDING SITE FOR RESIDUE SO4 B 401
4AC4SOFTWAREMET C:147 , ILE C:148 , SER C:149 , HIS C:150 , GLU C:281 , LYS C:323 , LYS C:325BINDING SITE FOR RESIDUE SO4 C 401
5AC5SOFTWAREHIS B:10 , THR C:120 , LYS C:122 , TRP C:139BINDING SITE FOR RESIDUE SO4 C 402
6AC6SOFTWAREMET D:147 , ILE D:148 , SER D:149 , HIS D:150 , GLU D:281 , LYS D:323 , LYS D:325 , HOH D:537BINDING SITE FOR RESIDUE SO4 D 401
7AC7SOFTWAREHIS A:10 , SER D:119 , THR D:120 , LYS D:122 , TRP D:139BINDING SITE FOR RESIDUE SO4 D 402
8AC8SOFTWARETRP D:175 , LYS D:176 , THR D:177 , GLN D:204 , ASN D:206 , LYS D:207 , PHE D:208 , LEU D:226 , PRO D:227 , ARG D:268BINDING SITE FOR RESIDUE 96P D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G8O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G8O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G8O)

(-) Exons   (0, 0)

(no "Exon" information available for 4G8O)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4g8oa_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhh.......eeeeeeeeee.......hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh......hhhhhhh.....eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.hhh.eeeeeeee......hhhhhh..hhhhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh..................eeeeeeeeee.....eee....eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8o A   4 APSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVALALQKVKIEVNESPEEIIIDRPFLFVVRHNPTGTVLFMGQVMEP 379
                                    13        23        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       350       360       370         
                                                                                                                                                                                                                                                                                                                                                                 331|                              
                                                                                                                                                                                                                                                                                                                                                                  349                              


Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4g8ob_ B: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhh.......eeeeeeeeee.......hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh......hhhhhhh.....eeeeeeeee.............eeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.hhh.eeeeeeee......hhhhhh..hhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhh...hhhhh..................eeeeeeeeee.....eee....eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8o B   4 APSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVALALQKVKIEVNESPEEIIIDRPFLFVVRHNPTGTVLFMGQVMEP 379
                                    13        23        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       350       360       370         
                                                                                                                                                                                                                                                                                                                                                                 331|                              
                                                                                                                                                                                                                                                                                                                                                                  349                              


Chain C from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4g8oc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhh.......eeeeeeeeee.......hhhhhhhhhhh...eee...hhhhhhhhhhhhhhh........hhhhhh......eeeeeeeee.............eeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.hhh.eeeeeeee......hhhhhh..hhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhh...hhhhh..................eeeeeeeeee............eeee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8o C   4 APSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVALALQKVKIEVNESVIVSARMAPEEIIIDRPFLFVVRHNPTGTVLFMGQVMEP 379
                                    13        23        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       342       352       362       372       
                                                                                                                                                                                                                                                                                                                                                                 331|                                      
                                                                                                                                                                                                                                                                                                                                                                  341                                      


Chain D from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4g8od_ D: automated matches                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeeeeeee.......hhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh......hhhhhhh.....eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeeee.....eeeeeeee.hhh.eeeeeeee......hhhhhh..hhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh.......................eeeeeeeeeeee....eeeee...eeee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g8o D   4 APSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQFQADFTSLSDQEPLHVALALQKVKIEVNESVIVSARMAPEEIIIDRPFLFVVRHNPTGTVLFMGQVMEP 379
                                    13        23        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       342       352       362       372       
                                                                                                                                                                                                                                                                                                                                                                 331|                                      
                                                                                                                                                                                                                                                                                                                                                                  341
   Legend:   → Mismatch (orange background)
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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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G8O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G8O)

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)

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  4g8o
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  PAI1_HUMAN | P05121
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAI1_HUMAN | P05121: 1a7c 1b3k 1c5g 1db2 1dvm 1dvn 1lj5 1oc0 3cvm 3eox 3pb1 3q02 3q03 3r4l 3ut3 4aqh 4g8r 4ic0 5brr 9pai

(-) Related Entries Specified in the PDB File

1b3k THE ACTIVE CONFORMATION OF PLASMINOGEN ACTIVATOR INHIBITOR 1
4g8r