+Open data
-Basic information
Entry | Database: PDB / ID: 2knm | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the cyclotide cycloviolacin O2 | ||||||
Components | Cycloviolacin-O2 | ||||||
Keywords | PLANT PROTEIN / cyclotide / cyclic cystine knot / circular protein / Cytolysis / Disulfide bond / Hemolysis / Knottin / Plant defense | ||||||
Function / homology | Cyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / killing of cells of another organism / Cycloviolacin-O2 Function and homology information | ||||||
Biological species | Viola odorata (plant) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Rosengren, K. | ||||||
Citation | Journal: Chembiochem / Year: 2009 Title: The conserved glu in the cyclotide cycloviolacin O2 has a key structural role. Authors: Goransson, U. / Herrmann, A. / Burman, R. / Haugaard-Jonsson, L.M. / Rosengren, K.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2knm.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2knm.ent.gz | 142.8 KB | Display | PDB format |
PDBx/mmJSON format | 2knm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/2knm ftp://data.pdbj.org/pub/pdb/validation_reports/kn/2knm | HTTPS FTP |
---|
-Related structure data
Related structure data | 2knnC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 3167.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Viola odorata (plant) / References: UniProt: P58434 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR solution structure of the cytotoxic cyclotide cycloviolacin O2 isolated from Viola odorata. This peptide is naturally head-to-tail cyclic, i.e. has a peptide bond between the N- and C-termini. | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||
Sample conditions | pH: 6.1 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: Structures were calculated using torsion angle dynamics within CNS and subsequently refined and energy minimised using cartesian dynamics in explicit water. | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 155 / NOE intraresidue total count: 0 / NOE long range total count: 38 / NOE medium range total count: 31 / NOE sequential total count: 86 / Hydrogen bond constraints total count: 32 / Protein chi angle constraints total count: 9 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 14 / Protein psi angle constraints total count: 0 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.273 Å |