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(-) Description

Title :  DENMOTOXIN: A THE THREE-FINGER TOXIN FROM COLUBRID SNAKE BOIGA DENDROPHILA WITH BIRD-SPECIFIC ACTIVITY
 
Authors :  J. Pawlak, R. M. Kini, E. A. Stura
Date :  26 May 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Three-Finger Toxin, Neurotoxin, Snake Venom (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Pawlak, S. P. Mackessy, B. G. Fry, M. Bhatia, G. Mourier, C. Fruchart-Gaillard, D. Servent, R. Menez, E. Stura, A. Menez, R. M. Kini
Denmotoxin, A Three-Finger Toxin From The Colubrid Snake Boiga Dendrophila (Mangrove Catsnake) With Bird-Specific Activity.
J. Biol. Chem. V. 281 29030 2006
PubMed-ID: 16864572  |  Reference-DOI: 10.1074/JBC.M605850200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DENMOTOXIN
    ChainsA, B
    Organism ScientificBOIGA DENDROPHILA
    Organism Taxid46286
    SecretionVENOM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2NA2Ligand/IonSODIUM ION
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NA-1Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2NA-1Ligand/IonSODIUM ION
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:13 , ASN A:14 , THR A:17 , SER A:19 , HIS A:31 , ARG A:55 , HOH A:317 , HOH A:385 , HOH A:414 , HOH A:416BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWARECYS B:13 , ASN B:14 , THR B:17 , SER B:19 , HIS B:31 , ARG B:55 , HOH B:308 , HOH B:324 , HOH B:351 , HOH B:384BINDING SITE FOR RESIDUE PO4 B 302
3AC3SOFTWAREHIS A:25 , ARG A:26 , HOH A:311 , HOH A:319 , HOH A:332 , HOH A:352 , HIS B:7 , ARG B:26BINDING SITE FOR RESIDUE PO4 A 303
4AC4SOFTWAREHIS A:7 , ARG A:26 , HIS B:25 , ARG B:26 , HOH B:347 , HOH B:363 , HOH B:420 , HOH B:438BINDING SITE FOR RESIDUE PO4 B 304
5AC5SOFTWAREASN A:14 , ARG A:15 , THR A:17 , SER A:19 , CYS A:21 , HOH A:379BINDING SITE FOR RESIDUE K A 305
6AC6SOFTWAREASN B:14 , ARG B:15 , THR B:17 , SER B:19 , CYS B:21BINDING SITE FOR RESIDUE K B 306
7AC7SOFTWAREHOH A:429 , SER B:19 , ASN B:20BINDING SITE FOR RESIDUE NA B 307
8AC8SOFTWARESER A:19 , ASN A:20 , HOH A:394BINDING SITE FOR RESIDUE NA A 308

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:10 -A:34
2A:13 -A:21
3A:27 -A:53
4A:57 -A:68
5A:69 -A:74
6B:10 -B:34
7B:13 -B:21
8B:27 -B:53
9B:57 -B:68
10B:69 -B:74

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H5F)

(-) Exons   (0, 0)

(no "Exon" information available for 2H5F)

(-) Sequences/Alignments

Asymmetric 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:75
 aligned with 3NB_BOIDE | Q06ZW0 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:75
                                    46        56        66        76        86        96       106     
            3NB_BOIDE    37 VGLPHGFCIQCNRKTWSNCSIGHRCLPYHMTCYTLYKPDENGEMKWAVKGCARMCPTAKSGERVKCCTGASCNSD 111
               SCOP domains d2h5fa1 A:3-77 Denmotoxin                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..ee..........eeeee...eeeeeee.......eeeeeeee..........eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2h5f A   3 VGLPHGFCIQCNRKTWSNCSIGHRCLPYHMTCYTLYKPDENGEMKWAVKGCARMCPTAKSGERVKCCTGASCNSD  77
                                    12        22        32        42        52        62        72     

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with 3NB_BOIDE | Q06ZW0 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:74
                                    47        57        67        77        87        97       107    
            3NB_BOIDE    38 GLPHGFCIQCNRKTWSNCSIGHRCLPYHMTCYTLYKPDENGEMKWAVKGCARMCPTAKSGERVKCCTGASCNSD 111
               SCOP domains d2h5fb_ B: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..ee..........eeeee...eeeeeeee.....eeeeeeeee..........eeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2h5f B   4 GLPHGFCIQCNRKTWSNCSIGHRCLPYHMTCYTLYKPDENGEMKWAVKGCARMCPTAKSGERVKCCTGASCNSD  77
                                    13        23        33        43        53        63        73    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H5F)

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (3NB_BOIDE | Q06ZW0)
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.

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