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(-) Description

Title :  CRYSTAL STRUCTURE OF COBROTOXIN
 
Authors :  X. Lou, X. Tu, J. Wang, M. Teng, L. Niu, Q. Liu, Q. Huang, Q. Hao
Date :  03 Dec 03  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.87
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atomic Resolution, Short-Chain Neurotoxin, Naja Atra, Copper Ion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Lou, Q. Liu, X. Tu, J. Wang, M. Teng, L. Niu, D. J. Schuller, Q. Huang, Q. Hao
The Atomic Resolution Crystal Structure Of Atratoxin Determined By Single Wavelength Anomalous Diffraction Phasing
J. Biol. Chem. V. 279 39094 2004
PubMed-ID: 15252034  |  Reference-DOI: 10.1074/JBC.M403863200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COBROTOXIN
    Chains: A, B
    Organism Common: CHINESE COBRA
    Organism Scientific: NAJA ATRA
    Organism Taxid: 8656
    Synonym: ATRATOXIN, CBT, SHORT NEUROTOXIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CU12Ligand/IonCOPPER (II) ION
3EOH2Ligand/IonETHANOL
4NA2Ligand/IonSODIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:38 , CL A:401 , HOH A:1241 , HIS B:4 , ARG B:59 , ASN B:62BINDING SITE FOR RESIDUE CU B 301
02AC2SOFTWAREHIS A:4 , PRO A:12 , ARG A:59 , ASN A:62 , NA A:501 , HOH A:1219 , GLU B:38 , HOH B:360BINDING SITE FOR RESIDUE CU A 302
03AC3SOFTWAREGLU A:2 , ASP A:58 , CU A:307 , HOH A:1205 , HOH A:1206 , HIS B:32BINDING SITE FOR RESIDUE CU A 303
04AC4SOFTWAREGLU A:51 , HOH A:1270 , HOH A:1271BINDING SITE FOR RESIDUE CU A 304
05AC5SOFTWAREARG A:59 , SER B:8 , ARG B:36 , THR B:37BINDING SITE FOR RESIDUE CU A 305
06AC6SOFTWAREASP A:31 , HIS A:32 , GLU B:2 , ASP B:58 , HOH B:375 , HOH B:376BINDING SITE FOR RESIDUE CU A 306
07AC7SOFTWAREGLU A:2 , CU A:303 , HOH A:1205 , HOH A:1206 , HOH A:1208 , HOH A:1218 , HOH A:1281 , ASP B:31BINDING SITE FOR RESIDUE CU A 307
08AC8SOFTWARELYS A:27 , LYS A:47 , CL A:401 , HIS B:4 , THR B:14 , ARG B:59BINDING SITE FOR RESIDUE CU A 308
09AC9SOFTWAREGLU A:2 , HOH A:1206 , TRP B:29BINDING SITE FOR RESIDUE CU B 309
10BC1SOFTWARESER A:8 , ARG A:36 , THR A:37 , HOH A:1252BINDING SITE FOR RESIDUE CU A 310
11BC2SOFTWAREASN A:48 , HOH A:1247 , HOH A:1264 , HOH A:1265 , HOH A:1286BINDING SITE FOR RESIDUE CU A 311
12BC3SOFTWAREGLY A:19 , HOH A:1203 , HOH A:1237 , ARG B:30 , HOH B:392 , HOH B:394BINDING SITE FOR RESIDUE CU A 312
13BC4SOFTWARELYS A:27 , GLU A:38 , CU A:308 , HIS B:4 , ARG B:59 , CU B:301BINDING SITE FOR RESIDUE CL A 401
14BC5SOFTWAREPRO A:12 , ASN A:62 , CU A:302 , HOH A:1214 , ASN B:5 , HOH B:322 , HOH B:360BINDING SITE FOR RESIDUE NA A 501
15BC6SOFTWARETHR A:14 , LYS B:27 , GLU B:38 , HOH B:342BINDING SITE FOR RESIDUE NA A 502
16BC7SOFTWARESER A:8 , SER A:9 , LYS A:47 , ASN A:48 , HOH A:1265 , HOH A:1304 , HOH A:1317 , HOH A:1340BINDING SITE FOR RESIDUE EOH A 1201
17BC8SOFTWARECYS A:43 , SER A:45 , VAL A:46 , HOH A:1268BINDING SITE FOR RESIDUE EOH A 1202

(-) 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 1V6P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V6P)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SNAKE_TOXINPS00272 Snake toxins signature.3S1CB_NAJAT61-79
 		  2A:40-58
B:40-58

(-) Exons   (0, 0)

(no "Exon" information available for 1V6P)

(-) 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 3S1CB_NAJAT | P60770 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:62
                                    31        41        51        61        71        81  
           3S1CB_NAJAT   22 LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN 83
               SCOP domains d1v6pa_ A: Cobrotoxin II (ct2)                                 SCOP domains
               CATH domains 1v6pA00 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
                  1v6p A  1 LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN 62
                                    10        20        30        40        50        60  


Chain B from PDB  Type:PROTEIN  Length:62
 aligned with 3S1CB_NAJAT | P60770 from UniProtKB/Swiss-Prot  Length:83

    Alignment length:62
                                    31        41        51        61        71        81  
           3S1CB_NAJAT   22 LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN 83
               SCOP domains d1v6pb_ B: Cobrotoxin II (ct2)                                 SCOP domains
               CATH domains 1v6pB00 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
                  1v6p B  1 LECHNQQSSQTPTTTGCSGGETNCYKKRWRDHRGYRTERGCGCPSVKNGIEINCCTTDRCNN 62
                                    10        20        30        40        50        60
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V6P)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (3S1CB_NAJAT | P60770)
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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 Related Entries

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        3S1CB_NAJAT | P60770: 1cod 1coe

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