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(-) Description

Title :  CRYSTAL STRUCTURE OF FACTOR IXA VARIANT K98T IN COMPLEX WITH EGR-CHLOROMETHYLKETONE
 
Authors :  L. H. Kristensen, H. Brandstetter
Date :  13 Apr 16  (Deposition) - 01 Jun 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  E,S
Keywords :  Blood Clotting, Hydrolase, Glycoprotein, Haemostasis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. H. Kristensen, O. H. Olsen, G. E. Blouse, H. Brandstetter
Releasing The Brakes In Coagulation Factor Ixa By Co-Operative Maturation Of The Substrate-Binding Site.
Biochem. J. V. 473 2395 2016
PubMed-ID: 27208168  |  Reference-DOI: 10.1042/BCJ20160336

(-) Compounds

Molecule 1 - COAGULATION FACTOR IX
    Chains: E
    EC Number: 3.4.21.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: NICO21
    Gene: F9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FRAGMENT: EGF2 DOMAIN, RESIDUES 133-191
    Synonym: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC
 
Molecule 2 - COAGULATION FACTOR IX
    Chains: S
    EC Number: 3.4.21.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: NICO21
    Gene: F9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FRAGMENT: CATALYTIC DOMAIN, RESIDUES 227-461
    Synonym: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : ES

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
10GJ1Ligand/IonL-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE
2CA1Ligand/IonCALCIUM ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU S:70 , ASN S:72 , GLU S:75 , GLU S:77 , GLU S:80 , HOH S:419binding site for residue CA S 301
2AC2SOFTWAREHIS S:57 , TYR S:99 , ASP S:189 , SER S:190 , GLN S:192 , GLY S:193 , SER S:195 , SER S:214 , TRP S:215 , GLY S:216 , GLU S:219 , GLY S:226 , HOH S:407 , HOH S:413 , HOH S:422 , HOH S:462 , HOH S:500 , HOH S:526 , HOH S:528binding site for residue 0GJ S 302
3AC3SOFTWARELEU S:153 , VAL S:154 , GLN S:156binding site for residue DMS S 303

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1E:88 -E:99
2E:95 -E:109
3E:111 -E:124
4E:132 -S:122
5S:42 -S:58
6S:168 -S:182
7S:191 -S:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JB8)

(-) Exons   (0, 0)

(no "Exon" information available for 5JB8)

(-) 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 E from PDB  Type:PROTEIN  Length:51
                                                                                    
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeee.....eeee....eee......eee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                5jb8 E   88 CNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVS  138
                                    97       107       117       127       137 


Chain S from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee......eeeeeee..eeeehhhhh......eeee............eeeeeeeeee...............eeeee................hhhhhhhhhhh.eeeeee..............eeeeeeeehhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jb8 S   16 VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINTYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT  245
                                    25        35|       46        56    |   65        75        85        95||     103       113       123      |131       141   ||  152       162       172       182  |    190       200       210      |221|      230       240     
                                              35|                     60A                                 95A|                               129A|             145|                                  184A 188A                          217|  |                        
                                               37                                                          95B                                129B              147                                                                      219  |                        
                                                                                                                                                                                                                                           221A
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5JB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JB8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JB8)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA9_HUMAN | P00740: 1cfh 1cfi 1edm 1ixa 1mgx 1nl0 1rfn 2wph 2wpi 2wpj 2wpk 2wpl 2wpm 3kcg 3lc3 3lc5 4wm0 4wma 4wmb 4wmi 4wmk 4wn2 4wnh 4yzu 4z0k 4zae 5egm 5f84 5f85 5f86 5jb9 5jba 5jbb 5jbc 5tno 5tnt

(-) Related Entries Specified in the PDB File

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