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- PDB-1chv: ELUCIDATION OF THE SOLUTION STRUCTURE OF CARDIOTOXIN ANALOGUE V F... -

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Entry
Database: PDB / ID: 1chv
TitleELUCIDATION OF THE SOLUTION STRUCTURE OF CARDIOTOXIN ANALOGUE V FROM THE TAIWAN COBRA (NAJA NAJA ATRA) VENOM
ComponentsPROTEIN (CARDIOTOXIN ANALOGUE V)
KeywordsTOXIN / CARDIOTOXINS / CYTOTOXINS
Function / homology
Function and homology information


other organism cell membrane / ion channel regulator activity / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja atra (Chinese cobra)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsJayaraman, G. / Kumar, T.K.S. / Tsai, C.C. / Yu, C.
Citation
Journal: Protein Sci. / Year: 2000
Title: Elucidation of the solution structure of cardiotoxin analogue V from the Taiwan cobra (Naja naja atra)--identification of structural features important for the lethal action of snake venom cardiotoxins
Authors: Jayaraman, G. / Kumar, T.K.S. / Tsai, C.C. / Chou, S.H. / Ho, C.L. / Yu, C.
#1: Journal: Toxicon / Year: 1997
Title: Cardiotoxin-like basic protein (CLBP) from Naja naja atra is not a cardiotoxin.
Authors: Sivaraman, T. / Kumar, T.K. / Yang, P.W. / Yu, C.
#2: Journal: J.Biomol.Struct.Dyn. / Year: 1997
Title: Snake venom cardiotoxins-structure, dynamics, function and folding.
Authors: Kumar, T.K. / Jayaraman, G. / Lee, C.S. / Arunkumar, A.I. / Sivaraman, T. / Samuel, D. / Yu, C.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 1995
Title: Sequence comparison and computer modelling of cardiotoxins and cobrotoxin isolated from Taiwan cobra.
Authors: Chiou, S.H. / Hung, C.C. / Huang, H.C. / Chen, S.T. / Wang, K.T. / Yang, C.C.
#4: Journal: Biochem.Int. / Year: 1985
Title: Amino acid sequence of a cardiotoxin-like basic polypeptide (CLBP) with low cytotoxic activity isolated from the venom of the Formosan cobra (Naja naja atra).
Authors: Takechi, M. / Tanaka, Y. / Hayashi, K.
History
DepositionMar 30, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: PROTEIN (CARDIOTOXIN ANALOGUE V)


Theoretical massNumber of molelcules
Total (without water)6,8211
Polymers6,8211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1minimized average structure

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Components

#1: Protein PROTEIN (CARDIOTOXIN ANALOGUE V)


Mass: 6821.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CTX V OBTAINED FROM THE SNAKE (NAJA NAJA ATRA) VENOM
Source: (natural) Naja atra (Chinese cobra) / References: UniProt: P07525
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY
NMR detailsText: MEAN STRUCTURE. NULL

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Sample preparation

DetailsContents: 90% H2O AND 10% D2O
Sample conditionspH: 3 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORNILGES,KUSEWSKI,BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINE.INP
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 1

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