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 :  ERABUTOXIN
 
Authors :  V. Nastopoulos, P. N. Kanellopoulos, D. Tsernoglou
Date :  16 Jan 98  (Deposition) - 16 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Neurotoxin, Erabutoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Nastopoulos, P. N. Kanellopoulos, D. Tsernoglou
Structure Of Dimeric And Monomeric Erabutoxin A Refined At 1. 5 A Resolution.
Acta Crystallogr. , Sect. D V. 54 964 1998
PubMed-ID: 9757111  |  Reference-DOI: 10.1107/S0907444998005125
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERABUTOXIN A
    ChainsA, B
    Organism CommonBROAD-BANDED BLUE SEA KRAIT
    Organism ScientificLATICAUDA SEMIFASCIATA
    Organism Taxid8631
    Other DetailsJAPANESE SEA SNAKE
    SecretionVENOM

 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 1QKD)

(-) Sites  (0, 0)

(no "Site" information available for 1QKD)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:24
2A:17 -A:41
3A:43 -A:54
4A:55 -A:60
5B:3 -B:24
6B:17 -B:41
7B:43 -B:54
8B:55 -B:60

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QKD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QKD)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3S1EA_LATSE61-79
 
  2A:40-58
B:40-58

(-) Exons   (0, 0)

(no "Exon" information available for 1QKD)

(-) 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:62
 aligned with 3S1EA_LATSE | P60775 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:62
                                    31        41        51        61        71        81  
           3S1EA_LATSE   22 RICFNHQSSQPQTTKTCSPGESSCYNKQWSDFRGTIIERGCGCPTVKPGIKLSCCESEVCNN 83
               SCOP domains d1qkda_ A: Erabutoxin B (also neurotoxin B)                    SCOP domains
               CATH domains 1qkdA00 A:1-62 CD59                                            CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.........eee.......eeeeeeee..eeeeeeee.........eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------SNAKE_TOXIN        ---- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  1qkd A  1 RICFNHQSSQPQTTKTCSPGESSCYNKQWSDFRGTIIERGCGCPTVKPGIKLSCCESEVCNN 62
                                    10        20        30        40        50        60  

Chain B from PDB  Type:PROTEIN  Length:62
 aligned with 3S1EA_LATSE | P60775 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:62
                                    31        41        51        61        71        81  
           3S1EA_LATSE   22 RICFNHQSSQPQTTKTCSPGESSCYNKQWSDFRGTIIERGCGCPTVKPGIKLSCCESEVCNN 83
               SCOP domains d1qkdb_ B: Erabutoxin B (also neurotoxin B)                    SCOP domains
               CATH domains 1qkdB00 B:1-62 CD59                                            CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.........eee.......eeeeeeee..eeeeeeee.........eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------SNAKE_TOXIN        ---- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  1qkd B  1 RICFNHQSSQPQTTKTCSPGESSCYNKQWSDFRGTIIERGCGCPTVKPGIKLSCCESEVCNN 62
                                    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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QKD)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (3S1EA_LATSE | P60775)
biological process
    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.
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.
    GO:0035792    other organism postsynaptic membrane    A postsynaptic membrane that is part of another organism, i.e. a secondary organism with which the first organism is interacting. A postsynaptic membrane is a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters transmit the signal across the synaptic cleft to the postsynaptic membrane.

 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 1qkd)
 
  Sites
(no "Sites" information available for 1qkd)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qkd)
 

(-) 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
  1qkd
    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
  3S1EA_LATSE | P60775
    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
  3S1EA_LATSE | P60775
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        3S1EA_LATSE | P607751qke 2era 3era 5ebx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QKD)