+Open data
-Basic information
Entry | Database: PDB / ID: 5nq4 | |||||||||
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Title | Cytotoxin-1 in DPC-micelle | |||||||||
Components | Cytotoxin 1 | |||||||||
Keywords | TOXIN / cytolytic peptide / cobra venom / cytotoxyc activity / three-finger protein | |||||||||
Function / homology | Function and homology information other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Naja oxiana (Central Asian cobra) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Dubovskii, P.V. / Dubinnyi, M.A. / Volynsky, P.E. / Pustovalova, Y.E. / Konshina, A.G. / Utkin, Y.N. / Efremov, R.G. / Arseniev, A.S. | |||||||||
Citation | Journal: J. Biomol. Struct. Dyn. / Year: 2018 Title: Impact of membrane partitioning on the spatial structure of an S-type cobra cytotoxin. Authors: Dubovskii, P.V. / Dubinnyi, M.A. / Volynsky, P.E. / Pustovalova, Y.E. / Konshina, A.G. / Utkin, Y.N. / Arseniev, A.S. / Efremov, R.G. #1: Journal: Biochem. J. / Year: 2005 Title: Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins. Authors: Dubovskii, P.V. / Lesovoy, D.M. / Dubinnyi, M.A. / Konshina, A.G. / Utkin, Y.N. / Efremov, R.G. / Arseniev, A.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nq4.cif.gz | 374.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nq4.ent.gz | 321.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nq4_validation.pdf.gz | 364.2 KB | Display | wwPDB validaton report |
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Full document | 5nq4_full_validation.pdf.gz | 497.3 KB | Display | |
Data in XML | 5nq4_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 5nq4_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/5nq4 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/5nq4 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6831.339 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Naja oxiana (Central Asian cobra) / References: UniProt: P01451 |
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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 |
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Sample |
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Sample conditions | Ionic strength: 50 mM / Ionic strength err: 0.2 / PH err: 0.1 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 323 K / Temperature err: 0.1
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 Details: the structures are based on 517 NOE constraints, 160 hudrogen bond and 24 disulfide bond constraints, and 236 constraints for 193 angles | ||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |