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

(-) Description

Title :  CRYSTAL STRUCTURE OF A THREE FINGER TOXIN FROM SNAKE VENOM
 
Authors :  C. Jobichen, J. Sivaraman
Date :  06 Jun 12  (Deposition) - 07 Nov 12  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Three Finger Toxin, Venom Toxin, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. M. Girish, S. Kumar, L. Joseph, C. Jobichen, R. M. Kini, J. Sivaraman
Identification And Structural Characterization Of A New Three-Finger Toxin Hemachatoxin From Hemachatus Haemachatus Venom.
Plos One V. 7 48112 2012
PubMed-ID: 23144733  |  Reference-DOI: 10.1371/JOURNAL.PONE.0048112

(-) Compounds

Molecule 1 - CYTOTOXIN 1
    ChainsA, B
    Organism CommonRINGHALS
    Organism ScientificHEMACHATUS HAEMACHATUS
    Organism Taxid8626
    SynonymHEMOLYTIC PROTEIN 12B, THREE FINGER TOXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3VTS)

(-) Sites  (0, 0)

(no "Site" information available for 3VTS)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:22
2A:15 -A:39
3A:43 -A:54
4A:55 -A:60
5B:3 -B:22
6B:15 -B:39
7B:43 -B:54
8B:55 -B:60

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VTS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SBH_HEMHA38-58
 
  2A:38-58
B:38-58

(-) Exons   (0, 0)

(no "Exon" information available for 3VTS)

(-) 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:61
 aligned with 3SBH_HEMHA | B3EWH9 from UniProtKB/Swiss-Prot  Length:61

    Alignment length:61
                                    10        20        30        40        50        60 
            3SBH_HEMHA    1 LKCHNKLVPFLSKTCPEGKNLCYKMTLMKMPKIPIKRGCTDACPKSSLLVKVVCCNKDKCN 61
               SCOP domains d3vtsa_ A: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eee......eeeeeee..eeeeeeeeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3vts A  1 LKCHNKLVPFLSKTCPEGKNLCYKMTLMKMPKIPIKRGCTDACPKSSLLVKVVCCNKDKCN 61
                                    10        20        30        40        50        60 

Chain B from PDB  Type:PROTEIN  Length:61
 aligned with 3SBH_HEMHA | B3EWH9 from UniProtKB/Swiss-Prot  Length:61

    Alignment length:61
                                    10        20        30        40        50        60 
            3SBH_HEMHA    1 LKCHNKLVPFLSKTCPEGKNLCYKMTLMKMPKIPIKRGCTDACPKSSLLVKVVCCNKDKCN 61
               SCOP domains d3vtsb_ B: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......eee......eeeeeee..eeeeeeeeeee.........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3vts B  1 LKCHNKLVPFLSKTCPEGKNLCYKMTLMKMPKIPIKRGCTDACPKSSLLVKVVCCNKDKCN 61
                                    10        20        30        40        50        60 

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (3SBH_HEMHA | B3EWH9)
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0044179    hemolysis in other organism    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
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
(no "Ligands, Modified Residues, Ions" information available for 3vts)
 
  Sites
(no "Sites" information available for 3vts)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vts)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3vts
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  3SBH_HEMHA | B3EWH9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  3SBH_HEMHA | B3EWH9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3VTS)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3VTS)