Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BENZAMIDINE-INHIBITED 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 :  1.54
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein C Activator, Snake Venom Serine Proteinase, 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  (7, 8)

Asymmetric/Biological Unit (7, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BEN1Ligand/IonBENZAMIDINE
3CL1Ligand/IonCHLORIDE ION
4GOL1Ligand/IonGLYCEROL
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:95 , PRO A:147 , ASN A:148 , ALA A:178 , HOH A:1204BINDING SITE FOR RESIDUE NAG A 701
2AC2SOFTWAREASN A:96A , HOH A:1157BINDING SITE FOR RESIDUE NAG A 801
3AC3SOFTWAREASN A:38 , ARG A:60 , ASN A:63BINDING SITE FOR RESIDUE NDG A 901
4AC4SOFTWAREHIS A:57 , ARG A:60 , LYS A:192 , GLY A:193 , SER A:195 , BEN A:401 , HOH A:1046 , HOH A:1127BINDING SITE FOR RESIDUE SO4 A 301
5AC5SOFTWARELEU A:81 , ARG A:83 , ARG A:110 , HOH A:1031 , HOH A:1172BINDING SITE FOR RESIDUE ACT A 601
6AC6SOFTWAREARG A:82 , LEU A:92 , ASN A:93 , CYS A:245EBINDING SITE FOR RESIDUE CL A 1001
7AC7SOFTWAREASP A:189 , THR A:190 , SER A:195 , GLY A:216 , GLY A:217 , CYS A:220 , GLY A:226 , SO4 A:301BINDING SITE FOR RESIDUE BEN A 401
8AC8SOFTWAREARG A:56 , THR A:97 , ILE A:98 , TRP A:99 , HOH A:1034 , HOH A:1157BINDING SITE FOR RESIDUE GOL A 501

(-) 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 2AIQ)

(-) 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 2AIQ)

(-) 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 d2aiqa_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2aiqA01   2aiqA02 A:26-125,A:231-245 Trypsin-like serine proteases                                          2aiqA01 A:16-25,A:127-230 Trypsin-like serine proteases                                              2aiqA02        ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeee....eeeehhhhh....eeee............eee.eeeee...............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
                2aiq 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)
  - → 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: 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 2AIQ)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BEN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:218 - Pro A:219   [ RasMol ]  
    Ser A:146 - Pro A:147   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2aiq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  VSPCA_AGKCO | P09872
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.74
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  VSPCA_AGKCO | P09872
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VSPCA_AGKCO | P09872: 2aip

(-) Related Entries Specified in the PDB File

2aip THE SAME PROTEIN COMPLEXED WITH BENZAMIDINE INHIBITOR