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- PDB-1h5o: Solution structure of Crotamine, a neurotoxin from Crotalus duris... -

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Basic information

Entry
Database: PDB / ID: 1h5o
TitleSolution structure of Crotamine, a neurotoxin from Crotalus durissus terrificus
ComponentsCrotamine
KeywordsTOXIN / SODIUM CHANNEL AFFECTING TOXIN / VENOM
Function / homology
Function and homology information


: / defense response to fungus / potassium channel regulator activity / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Myotoxin / Myotoxin, crotamine / Myotoxins signature. / Myotoxins family profile. / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodSOLUTION NMR / simulated annealing
AuthorsNicastro, G. / Franzoni, L. / De Chiara, C. / Mancin, C.A. / Giglio, J.R. / Spisni, A.
Citation
Journal: Eur.J.Biochem. / Year: 2003
Title: Solution Structure of Crotamine, a Na+ Channel Affecting Toxin from Crotalus Durissus Terrificus Venom
Authors: Nicastro, G. / Franzoni, L. / De Chiara, C. / Mancin, A.C.A. / Giglio, J.R. / Spisni, A.
#1: Journal: Toxicon / Year: 1998
Title: The Analgesic Activity of Crotamine,A Neurotoxin from Crotalus Durissus Terrificus Venom:A Biochemical and Pharmacological Study
Authors: Mancin, A.C. / Soares, A.M. / Andriao-Escarso, S.H. / Faca, V.M. / Greene, L.J. / Zuccolotto, S. / Pela, I.R. / Giglio, J.R.
History
DepositionMay 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Derived calculations / Other ...Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name
Revision 2.0Dec 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_src_nat / pdbx_modification_feature / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity_name_com.name / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _pdbx_validate_close_contact.PDB_model_num / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_angle.PDB_model_num / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crotamine


Theoretical massNumber of molelcules
Total (without water)4,9031
Polymers4,9031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 50LEAST RESTRAINT VIOLATION, LEAST RESIDUAL DEVIATIONS FROM IDEALIZED GEOMETRY
Representative

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Components

#1: Protein/peptide Crotamine / Crt / Myotoxin


Mass: 4902.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VENOM OF THE RATTLESNAKE CROTALUS DURISSUS TERRIFICUS
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: Q9PWF3
Compound detailsEXTREMELY RAPID ACTING TOXIN THAT CAUSES MUSCLE NECROSIS. DISABLES PREY BY CAUSING INSTANTANEOUS ...EXTREMELY RAPID ACTING TOXIN THAT CAUSES MUSCLE NECROSIS. DISABLES PREY BY CAUSING INSTANTANEOUS PARALYSIS OF HIND LIMBS AND DEATH BY PARALYSIS OF THE DIAPHRAGM.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131DQF-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H-1H 2D NMR ON THE NATURAL TOXIN EXTRACTED FROM THE SNAKE VENOM.

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Sample preparation

DetailsContents: 1MM CROTAMINE, H2O/TFE (70/30)
Sample conditionspH: 4 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
DiscoverBIOSYMrefinement
MSI DISCOVERDISCOVERstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE JRNL CITATION
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, LEAST RESIDUAL DEVIATIONS FROM IDEALIZED GEOMETRY
Conformers calculated total number: 50 / Conformers submitted total number: 26

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