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(-) Description

Title :  STRUCTURE OF SCORPION NEUROTOXIN BMK M4
 
Authors :  X. L. He, H. M. Li, X. Q. Liu, Z. H. Zeng, D. C. Wang
Date :  11 Nov 98  (Deposition) - 17 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Neurotoxin, Sodium Channel Inhibitor, Scorpion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. L. He, H. M. Li, Z. H. Zeng, X. Q. Liu, M. Wang, D. C. Wang
Crystal Structures Of Two Alpha-Like Scorpion Toxins: Non-Proline Cis Peptide Bonds And Implications For New Binding Site Selectivity On The Sodium Channel.
J. Mol. Biol. V. 292 125 1999
PubMed-ID: 10493862  |  Reference-DOI: 10.1006/JMBI.1999.3036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (NEUROTOXIN BMK M4)
    Chains: A
    Organ: TAIL
    Organism Common: CHINESE SCORPION
    Organism Scientific: MESOBUTHUS MARTENSII
    Organism Taxid: 34649
    Secretion: VENOM
    Synonym: BMK-IV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:11 , CYS A:12 , VAL A:13 , GLY A:18 , ASN A:19 , TRP A:38 , ARG A:58 , CYS A:63 , HOH A:70 , HOH A:180BINDING SITE FOR RESIDUE ACT A 65
2AC2SOFTWAREARG A:41 , HOH A:120BINDING SITE FOR RESIDUE ACT A 66
3AC3SOFTWAREHOH A:172 , HOH A:174 , HOH A:181 , HOH A:185BINDING SITE FOR RESIDUE ACT A 67
4AC4SOFTWAREHOH A:95BINDING SITE FOR RESIDUE ACT A 68
5AC5SOFTWARELYS A:50 , HIS A:64 , HOH A:146BINDING SITE FOR RESIDUE ACT A 69

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:12 -A:63
2A:16 -A:36
3A:22 -A:46
4A:26 -A:48

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:9 -Glu A:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SN4)

(-) Exons   (0, 0)

(no "Exon" information available for 1SN4)

(-) 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:64
 aligned with SCX4_MESMA | P58328 from UniProtKB/Swiss-Prot  Length:64

    Alignment length:64
                                    10        20        30        40        50        60    
            SCX4_MESMA    1 VRDAYIAKPENCVYHCAGNEGCNKLCTDNGAESGYCQWGGRYGNACWCIKLPDDVPIRVPGKCH 64
               SCOP domains d1sn4a_ A: Scorpion toxin                                        SCOP domains
               CATH domains 1sn4A00 A:1-64  [code=3.30.30.10, no name defined]               CATH domains
               Pfam domains -Toxin_3-1sn4A01 A:2-55                                --------- Pfam domains
         Sec.struct. author .eeee............hhhhhhhhhhhh...eeeeeee...eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  1sn4 A  1 VRDAYIAKPENCVYHCAGNEGCNKLCTDNGAESGYCQWGGRYGNACWCIKLPDDVPIRVPGKCH 64
                                    10        20        30        40        50        60    


Chain A from PDB  Type:PROTEIN  Length:64
 aligned with SCX9_MESMA | P45698 from UniProtKB/Swiss-Prot  Length:79

    Alignment length:64
                                    24        34        44        54        64        74    
            SCX9_MESMA   15 VRDAYIAKPENCVYHCATNEGCNKLCTDNGAESGYCQWGGRYGNACWCIKLPDRVPIRVPGKCH 78
               SCOP domains d1sn4a_ A: Scorpion toxin                                        SCOP domains
               CATH domains 1sn4A00 A:1-64  [code=3.30.30.10, no name defined]               CATH domains
               Pfam domains -Toxin_3-1sn4A01 A:2-55                                --------- Pfam domains
         Sec.struct. author .eeee............hhhhhhhhhhhh...eeeeeee...eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  1sn4 A  1 VRDAYIAKPENCVYHCAGNEGCNKLCTDNGAESGYCQWGGRYGNACWCIKLPDDVPIRVPGKCH 64
                                    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, 1)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Knottin_1 (78)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SCX4_MESMA | P58328)
molecular function
    GO:0008200    ion channel inhibitor activity    Stops, prevents, or reduces the activity of an ion channel.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
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.

Chain A   (SCX9_MESMA | P45698)
molecular function
    GO:0008200    ion channel inhibitor activity    Stops, prevents, or reduces the activity of an ion channel.
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
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

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

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(-) Related Entries Specified in the PDB File

1sn1