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(-) Description

Title :  CRYSTAL STRUCTURE OF NATIVE PROTEIN C ACTIVATOR FROM THE VENOM OF COPPERHEAD SNAKE AGKISTRODON CONTORTRIX CONTORTRIX
 
Authors :  M. T. Murakami, R. K. Arni
Date :  30 Jul 05  (Deposition) - 06 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein C Activator, Snake Venom, Trypsin-Like Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. T. Murakami, R. K. Arni
Thrombomodulin-Independent Activation Of Protein C And Specificity Of Hemostatically Active Snake Venom Serine Proteinases: Crystal Structures Of Native And Inhibited Agkistrodon Contortrix Contortrix Protein C Activator.
J. Biol. Chem. V. 280 39309 2005
PubMed-ID: 16162508  |  Reference-DOI: 10.1074/JBC.M508502200

(-) Compounds

Molecule 1 - PROTEIN C ACTIVATOR
    Chains: A
    EC Number: 3.4.21.74
    Organism Common: SOUTHERN COPPERHEAD
    Organism Scientific: AGKISTRODON CONTORTRIX CONTORTRIX
    Organism Taxid: 8713
    Strain: CONTORTRIX
    Synonym: VENOMBIN A, ANCROD, ACC-C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:147 , ASN A:148BINDING SITE FOR RESIDUE NAG A 601
2AC2SOFTWAREASN A:96A , GOL A:401BINDING SITE FOR RESIDUE NAG A 701
3AC3SOFTWAREASN A:38 , ARG A:60BINDING SITE FOR RESIDUE NDG A 801
4AC4SOFTWAREHIS A:57 , ARG A:60 , LYS A:192 , GLY A:193 , SER A:195 , HOH A:846 , HOH A:921 , HOH A:976BINDING SITE FOR RESIDUE SO4 A 301
5AC5SOFTWAREASN A:127 , PRO A:129 , SER A:131 , SER A:134 , ASN A:202 , GLN A:208 , ARG A:223 , HOH A:870 , HOH A:971BINDING SITE FOR RESIDUE SO4 A 302
6AC6SOFTWAREARG A:82 , CYS A:91 , LEU A:92 , ASN A:93 , THR A:245D , CYS A:245E , HOH A:860 , HOH A:984BINDING SITE FOR RESIDUE SO4 A 303
7AC7SOFTWARELEU A:81 , ARG A:83 , ARG A:110BINDING SITE FOR RESIDUE ACT A 501
8AC8SOFTWAREARG A:56 , THR A:97 , TRP A:99 , NAG A:701 , HOH A:834BINDING SITE FOR RESIDUE GOL A 401

(-) 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  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:146 -Pro A:147
2Asn A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AIP)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.VSPCA_AGKCO1-222  1A:16-243
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.VSPCA_AGKCO171-182  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 2AIP)

(-) 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:231
 aligned with VSPCA_AGKCO | P09872 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
         VSPCA_AGKCO      1 VIGGDECNINEHRFLALVYANGSLCGGTLINQEWVLTARHCDRGNMRIYLGMHNLKVLNKDALRRFPKEKYFCLNTRNDTIWDKDIMLIRLNRPVRNSAHIAPLSLPSNPPSVGSVCRIMGWGTITSPNATLPDVPHCANINILDYAVCQAAYKGLAATTLCAGILEGGKDTCKGDSGGPLICNGQFQGILSVGGNPCAQPRKPGIYTKVFDYTDWIQSIISGNTDATCPP  231
               SCOP domains d2aipa_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2aipA01   2aipA02 A:26-125,A:231-245 Trypsin-like serine proteases                                          2aipA01 A:16-25,A:127-230 Trypsin-like serine proteases                                              2aipA02        ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeee..eeeehhhhh....eeee............eee.eeeeee..............eeeee........................eeeeee...............eeeeeeeehhhhhhhhh......eeeee...............eeee..eeeeeeeee..........eeeee...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 1-222                                                                                                                                                                                     --------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2aip A   16 VIGGDECNINEHRFLALVYANGSLCGGTLINQEWVLTARHCDRGNMRIYLGMHNLKVLNKDALRRFPKEKYFCLNTRNDTIWDKDIMLIRLNRPVRNSAHIAPLSLPSNPPSVGSVCRIMGWGTITSPNATLPDVPHCANINILDYAVCQAAYKGLAATTLCAGILEGGKDTCKGDSGGPLICNGQFQGILSVGGNPCAQPRKPGIYTKVFDYTDWIQSIISGNTDATCPP 245G
                                    25        36|       47        57  ||    68        78        88       |97       107       117       128||     139       149       159       169  ||   180      |188       198   ||  212      221A       231       241    ||245F|
                                             34||                    60|                               96A                           125| ||                                      172|         186A|             202|           221A                     245A||||||
                                              36|                     62                                                              127 ||                                       174          186B              207                                     245B|||||
                                               38                                                                                       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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AIP)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VSPCA_AGKCO | P09872)
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

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        VSPCA_AGKCO | P09872: 2aiq

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