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(-) Description

Title :  X-RAY STRUCTURE AT 1.55 A OF TOXIN GAMMA, A CARDIOTOXIN FROM NAJA NIGRICOLLIS VENOM. CRYSTAL PACKING REVEALS A MODEL FOR INSERTION INTO MEMBRANES
 
Authors :  A. Bilwes, B. Rees, D. Moras
Date :  24 Nov 93  (Deposition) - 30 Apr 94  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A (2x),B (2x),C (2x)
Biol. Unit 2:  A (2x),B (2x),C (2x)
Biol. Unit 3:  A (2x),B (2x),C (2x)
Biol. Unit 4:  A (2x),B (2x),C (2x)
Keywords :  Cytotoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bilwes, B. Rees, D. Moras, R. Menez, A. Menez
X-Ray Structure At 1. 55 A Of Toxin Gamma, A Cardiotoxin From Naja Nigricollis Venom. Crystal Packing Reveals A Model For Insertion Into Membranes.
J. Mol. Biol. V. 239 122 1994
PubMed-ID: 8196041  |  Reference-DOI: 10.1006/JMBI.1994.1357
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GAMMA-CARDIOTOXIN
    Chains: A, B, C
    Engineered: YES
    Organism Common: SPITTING COBRA
    Organism Scientific: NAJA NIGRICOLLIS
    Organism Taxid: 8654

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A (2x)B (2x)C (2x)
Biological Unit 2 (2x): A (2x)B (2x)C (2x)
Biological Unit 3 (2x): A (2x)B (2x)C (2x)
Biological Unit 4 (2x): A (2x)B (2x)C (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1CL14Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:12 , LYS A:18BINDING SITE FOR RESIDUE CL A 102
02AC2SOFTWARELEU A:1BINDING SITE FOR RESIDUE CL A 120
03AC3SOFTWARELYS B:12 , CL B:106BINDING SITE FOR RESIDUE CL B 102
04AC4SOFTWARELYS B:12 , GLY B:37 , CYS B:38 , CL B:102BINDING SITE FOR RESIDUE CL B 106
05AC5SOFTWARELEU B:1 , LYS B:2 , LEU C:1BINDING SITE FOR RESIDUE CL B 120
06AC6SOFTWAREHOH A:291 , ARG B:36BINDING SITE FOR RESIDUE CL B 123
07AC7SOFTWARELYS C:12 , PRO C:15 , LYS C:18 , CL C:106BINDING SITE FOR RESIDUE CL C 102
08AC8SOFTWARELYS C:12 , CYS C:38 , CL C:102BINDING SITE FOR RESIDUE CL C 106
09AC9SOFTWARELYS A:44 , TRP B:11 , PRO C:43 , LYS C:44 , HOH C:151BINDING SITE FOR RESIDUE CL C 113
10BC1SOFTWARELYS B:16 , LYS C:16 , HOH C:150BINDING SITE FOR RESIDUE CL B 206
11BC2SOFTWAREARG A:36 , LYS C:50BINDING SITE FOR RESIDUE CL A 242
12BC3SOFTWAREARG A:27 , HOH A:288 , HOH A:292 , HOH A:304BINDING SITE FOR RESIDUE CL A 245
13BC4SOFTWAREARG A:27 , HOH A:304 , ARG C:27BINDING SITE FOR RESIDUE CL A 260
14BC5SOFTWARELYS B:18BINDING SITE FOR RESIDUE CL B 270

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:3 -A:21
2A:14 -A:38
3A:42 -A:53
4A:54 -A:59
5B:3 -B:21
6B:14 -B:38
7B:42 -B:53
8B:54 -B:59
9C:3 -C:21
10C:14 -C:38
11C:42 -C:53
12C:54 -C:59

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:8 -Pro A:9
2Pro B:8 -Pro B:9
3Pro C:8 -Pro C:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA1_NAJPA37-57
 
 		  3A:37-57
B:37-57
C:37-57
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA1_NAJPA37-57
 
 		  6A:37-57
B:37-57
C:37-57
Biological Unit 2 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA1_NAJPA37-57
 
 		  6A:37-57
B:37-57
C:37-57
Biological Unit 3 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA1_NAJPA37-57
 
 		  6A:37-57
B:37-57
C:37-57
Biological Unit 4 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3SA1_NAJPA37-57
 
 		  6A:37-57
B:37-57
C:37-57

(-) Exons   (0, 0)

(no "Exon" information available for 1TGX)

(-) 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:60
 aligned with 3SA1_NAJPA | P01468 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:60
                                    10        20        30        40        50        60
            3SA1_NAJPA    1 LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN 60
               SCOP domains d1tgxa_ A: gamma-Cardiotoxin                                 SCOP domains
               CATH domains 1tgxA00 A:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author eeeee....eeeee.....eeeeeeee.......eeeee........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  1tgx A  1 LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN 60
                                    10        20        30        40        50        60


Chain B from PDB  Type:PROTEIN  Length:60
 aligned with 3SA1_NAJPA | P01468 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:60
                                    10        20        30        40        50        60
            3SA1_NAJPA    1 LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN 60
               SCOP domains d1tgxb_ B: gamma-Cardiotoxin                                 SCOP domains
               CATH domains 1tgxB00 B:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author eeeee....eeeee.....eeeeeeee.......eeeee........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  1tgx B  1 LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN 60
                                    10        20        30        40        50        60


Chain C from PDB  Type:PROTEIN  Length:60
 aligned with 3SA1_NAJPA | P01468 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:60
                                    10        20        30        40        50        60
            3SA1_NAJPA    1 LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN 60
               SCOP domains d1tgxc_ C: gamma-Cardiotoxin                                 SCOP domains
               CATH domains 1tgxC00 C:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author eeeee....eeeee.....eeeeeeee.......eeeee........eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  1tgx C  1 LKCNQLIPPFWKTCPKGKNLCYKMTMRAAPMVPVKRGCIDVCPKSSLLIKYMCCNTDKCN 60
                                    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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (3SA1_NAJPA | P01468)
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.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0044218    other organism cell membrane    The cell membrane of a secondary organism with which the first organism is interacting.
    GO:0044279    other organism membrane    A membrane of a secondary organism with which the first organism is interacting.

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  1tgx
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        3SA1_NAJPA | P01468: 1cxn 1cxo

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