+Open data
-Basic information
Entry | Database: PDB / ID: 7o2k | ||||||
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Title | NMR solution structue of cytotoxin 2 from Naja Kaouthia | ||||||
Components | Cytotoxin 2 | ||||||
Keywords | TOXIN / S-type cytotoxin / cobra venom / three-finger protein / membrane-active polypeptide | ||||||
Function / homology | Snake cytotoxin, cobra-type / cytolysis / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / toxin activity / extracellular region / membrane / Cytotoxin 2 Function and homology information | ||||||
Biological species | Naja kaouthia (monocled cobra) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Dubinnyi, M.A. / Dubovskii, P.V. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: The omega-loop of cobra cytotoxins tolerates multiple amino acid substitutions. Authors: Dubinnyi, M.A. / Dubovskii, P.V. / Starkov, V.G. / Utkin, Y.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o2k.cif.gz | 340 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o2k.ent.gz | 292.1 KB | Display | PDB format |
PDBx/mmJSON format | 7o2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o2k_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 7o2k_full_validation.pdf.gz | 571.3 KB | Display | |
Data in XML | 7o2k_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 7o2k_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/7o2k ftp://data.pdbj.org/pub/pdb/validation_reports/o2/7o2k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6756.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P01445 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2 mM cytotoxin 2, 3 mM Cytotoxin 3, 90% H2O/10% D2O Details: 3 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 90% H2O/10% D2O Label: The mixture of CT3 and CT2 Naja kaouthia / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 mM / Ionic strength err: 0 / Label: Cytotoxins 2 and 3 / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 303 K / Temperature err: 1 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: 582 NOE constraints, 109 angular constraints, 27 H-bonds, 4 SS-bonds | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |