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Yorodumi- PDB-1zad: Structure of cytotoxin I (CTI) from Naja Oxiana in complex with D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zad | ||||||
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Title | Structure of cytotoxin I (CTI) from Naja Oxiana in complex with DPC micelle | ||||||
Components | Cytotoxin 1Cytotoxicity | ||||||
Keywords | TOXIN / antiparallel beta-sheet / beta-turn type I / beta-turn type II | ||||||
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 | Dubinnyi, M.A. / Pustovalova, Y.E. / Dubovskii, P.V. / Utkin, Y.N. / Konshina, A.G. / Efremov, R.G. / Arseniev, A.S. | ||||||
Citation | 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. #1: Journal: Biochemistry / Year: 2004 Title: Comparative study of structure and activity of cytotoxins from venom of the cobras Naja oxiana, Naja kaouthia, and Naja haje Authors: Feofanov, A.V. / Sharonov, G.V. / Dubinnyi, M.A. / Astapova, M.V. / Kudelina, I.A. / Dubovskii, P.V. / Rodionov, D.I. / Utkin, Y.N. / 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 | 1zad.cif.gz | 369 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zad.ent.gz | 319.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/1zad ftp://data.pdbj.org/pub/pdb/validation_reports/za/1zad | HTTPS FTP |
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-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: 6831.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja oxiana (Central Asian cobra) / Secretion: venom / References: UniProt: P01451 |
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-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 conditions | Ionic strength: 1 mM / pH: 6.0 / Pressure: ambient / Temperature: 323 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Flexible proline residues were used to distinguish Up/Down conformation of proline rings. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20 |