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- PDB-1kd6: Solution structure of the eukaryotic pore-forming cytolysin equin... -
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Basic information
Entry | Database: PDB / ID: 1kd6 | ||||||
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Title | Solution structure of the eukaryotic pore-forming cytolysin equinatoxin II | ||||||
![]() | EQUINATOXIN II | ||||||
![]() | MEMBRANE PROTEIN / cytolysin / pore formation / beta sandwich / toxin / sea anemone | ||||||
Function / homology | ![]() nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dyanamics distance geometry simulated annealing | ||||||
![]() | Hinds, M.G. / Zhang, W. / Anderluh, G. / Hansen, P.E. / Norton, R.S. | ||||||
![]() | ![]() Title: Solution structure of the eukaryotic pore-forming cytolysin equinatoxin II: implications for pore formation. Authors: Hinds, M.G. / Zhang, W. / Anderluh, G. / Hansen, P.E. / Norton, R.S. #1: ![]() Title: Sequence-specific resonance assignments of the potent cytolysin equinatoxin II Authors: Zhang, W. / Hinds, M.G. / Anderluh, G. / Hansen, P.E. / Norton, R.S. | ||||||
History |
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Remark 999 | SEQUENCE THERE ARE TWO NATURALLY OCCURING SEQUENCE VARIANTS P116D AND T212S FOR EQUINATOXIN II ...SEQUENCE THERE ARE TWO NATURALLY OCCURING SEQUENCE VARIANTS P116D AND T212S FOR EQUINATOXIN II P116D VARIANT OCCURS IN 50% OF MOLECULES FROM ACTINIA EQUINA AND THE T212S VARIANT IN ACTINA TENEBROSA. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 904.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 343.6 KB | Display | ![]() |
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Full document | ![]() | 532.9 KB | Display | |
Data in XML | ![]() | 78.4 KB | Display | |
Data in CIF | ![]() | 102.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 19859.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple resonance spectroscopy |
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Sample preparation
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Sample conditions | pH: 3.9 / Pressure: ambient / Temperature: 303 K | ||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dyanamics distance geometry simulated annealing Software ordinal: 1 Details: The structure is based on 3161 total restraints including 167 angle constraints, 42 hydrogen bonds, 534 sequential, 972 short range and 1346 long range distance constraints. | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations Conformers calculated total number: 250 / Conformers submitted total number: 20 |