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(-) Description

Title :  RUSSELL'S VIPER VENOM SERINE PROTEINASE, RVV-V (PPACK-BOUND FORM)
 
Authors :  D. Nakayama, Y. Ben Ammar, S. Takeda
Date :  05 Jun 11  (Deposition) - 07 Sep 11  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Proteinase, Glycosylation, Double Six-Stranded Beta-Barrels, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nakayama, Y. Ben Ammar, T. Miyata, S. Takeda
Structural Basis Of Coagulation Factor V Recognition For Cleavage By Rvv-V
Febs Lett. V. 585 3020 2011
PubMed-ID: 21871889  |  Reference-DOI: 10.1016/J.FEBSLET.2011.08.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIPERA RUSSELLI PROTEINASE RVV-V GAMMA
    Chains: A
    EC Number: 3.4.21.95
    Organism Common: SIAMESE RUSSELL'S VIPER
    Organism Scientific: DABOIA RUSSELLII SIAMENSIS
    Organism Taxid: 343250
    Synonym: FACTOR V-ACTIVATING PROTEINASE GAMMA, SNAKE VENOM FACTOR V ACTIVATOR GAMMA
    Tissue: VENOM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
10G61Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:245 , THR A:245BBINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWAREHIS A:57 , TYR A:172 , ASP A:189 , THR A:190 , CYS A:191 , GLY A:193 , SER A:195 , ALA A:214 , GLY A:215 , GLY A:216 , SER A:217 , GLU A:218 , CYS A:220 , ALA A:226BINDING SITE FOR RESIDUE 0G6 A 302

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:91 -A:245E
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SBK)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.VSPG_DABSI25-251  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.VSPG_DABSI63-68  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.VSPG_DABSI200-211  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 3SBK)

(-) 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:234
 aligned with VSPG_DABSI | P18965 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:236
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254      
          VSPG_DABSI     25 VVGGDECNINEHPFLVALYTSASSTIHCAGALINREWVLTAAHCDRRNIRIKLGMHSKNIRNEDEQIRVPRGKYFCLNTKFPNGLDKDIMLIRLRRPVTYSTHIAPVSLPSRSRGVGSRCRIMGWGKISTTEDTYPDVPHCTNIFIVKHKWCEPLYPWVPADSRTLCAGILKGGRDTCHGDSGGPLICNGEMHGIVAGGSEPCGQHLKPAVYTKVFDYNNWIQSIIAGNRTVTCPP  260
               SCOP domains d3sbka_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeeeee..eeeehhhhh...eeeee............eee.eeeee.........hhhhh.eeeee........................eeeeee.........--....eeeeeeeehhhhhhhhh........eeeee...............eeee..eeeeeeee...........eeeee...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 25-251                                                                                                                                                                                         --------- PROSITE (1)
                PROSITE (2) --------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3sbk A   16 VVGGDECNINEHPFLVALYTSASSTIHCAGALINREWVLTAAHCDRRNIRIKLGMHSKNIRNEDEQIRVPRGKYFCLNTKFPNGLDKDIMLIRLRRPVTYSTHIAPVSLPSRSRGVGSRCRIMGWGKISTTTY--PDVPHCTNIFIVKHKWCEPLYPWVPADSRTLCAGILKGGRDTCHGDSGGPLICNGEMHGIVAGGSEPCGQHLKPAVYTKVFDYNNWIQSIIAGNRTVTCPP 245G
                                    25        35 |      44        54     || 65        75        85        95|      104       114       124|| ||  136       146  |  | 156       166      |175       185 ||    193       207       217    |  226       236      245A||||||
                                               36A                      60|                               95A                           125| ||               149  |                 172A           186A|             202|           221A                     245A||||||
                                                                         62                                                              127 ||                  152                                 186B              207                                     245B|||||
                                                                                                                                           129|                                                                                                                 245C||||
                                                                                                                                            131                                                                                                                  245D|||
                                                                                                                                                                                                                                                                  245E||
                                                                                                                                                                                                                                                                   245F|
                                                                                                                                                                                                                                                                    245G
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SBK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VSPG_DABSI | P18965)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VSPG_DABSI | P18965: 3s9a 3s9b 3s9c

(-) Related Entries Specified in the PDB File

3s9a SAME PROTEIN WITHOUT INHIBITOR
3s9b SAME PROTEIN WITHOUT INHIBITOR
3s9c SAME PROTEIN COMPLEXED WITH THE FRAGMENT OF THE SUBSTRATE