[English] 日本語
Yorodumi- PDB-1px9: Solution structure of the native CnErg1 Ergtoxin, a highly specif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1px9 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the native CnErg1 Ergtoxin, a highly specific inhibitor of HERG channel | ||||||
Components | ergtoxin | ||||||
Keywords | TOXIN / alpha/beta molecular scaffold | ||||||
Function / homology | Function and homology information potassium channel inhibitor activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Centruroides noxius (Mexican scorpion) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Frenal, K. / Wecker, K. / Gurrola, G.B. / Possani, L.D. / Wolff, N. / Delepierre, M. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels. Authors: Frenal, K. / Xu, C.Q. / Wolff, N. / Wecker, K. / Gurrola, G.B. / Zhu, S.Y. / Chi, C.W. / Possani, L.D. / Tytgat, J. / Delepierre, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1px9.cif.gz | 18.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1px9.ent.gz | 13.5 KB | Display | PDB format |
PDBx/mmJSON format | 1px9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1px9_validation.pdf.gz | 241.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1px9_full_validation.pdf.gz | 241.3 KB | Display | |
Data in XML | 1px9_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 1px9_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/1px9 ftp://data.pdbj.org/pub/pdb/validation_reports/px/1px9 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 4746.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Centruroides noxius (Mexican scorpion) / Secretion: venom / References: UniProt: Q86QT3 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||
NMR details | Text: shigemi tube and nano-probe |
-Sample preparation
Details | Contents: 0.55 mg of lyophilized natural ErgTx / Solvent system: 0.160 mL, H2O/D2O 9:1, pH 3 |
---|---|
Sample conditions | pH: 3 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 452 distance constraints (252 are intraresidual NOE-derivated distance constraints, 200 are interresidual NOE-derivated distance constraints including ...Details: The structures are based on a total of 452 distance constraints (252 are intraresidual NOE-derivated distance constraints, 200 are interresidual NOE-derivated distance constraints including 49 long range), 13 3J and 10 hbonds | ||||||||||||||||
NMR representative | Selection criteria: fewest violations, lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy Conformers calculated total number: 10 / Conformers submitted total number: 1 |