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Open data
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Basic information
Entry | Database: PDB / ID: 2m7t | ||||||
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Title | Solution NMR Structure of Engineered Cystine Knot Protein 2.5D | ||||||
![]() | Cystine Knot Protein 2.5D | ||||||
![]() | PROTEIN BINDING / Protein Engineering / Cystine Knot / Knottin / CASP | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
![]() | Cochran, F.V. / Das, R. | ||||||
![]() | ![]() Title: Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Authors: Kryshtafovych, A. / Moult, J. / Bales, P. / Bazan, J.F. / Biasini, M. / Burgin, A. / Chen, C. / Cochran, F.V. / Craig, T.K. / Das, R. / Fass, D. / Garcia-Doval, C. / Herzberg, O. / Lorimer, ...Authors: Kryshtafovych, A. / Moult, J. / Bales, P. / Bazan, J.F. / Biasini, M. / Burgin, A. / Chen, C. / Cochran, F.V. / Craig, T.K. / Das, R. / Fass, D. / Garcia-Doval, C. / Herzberg, O. / Lorimer, D. / Luecke, H. / Ma, X. / Nelson, D.C. / van Raaij, M.J. / Rohwer, F. / Segall, A. / Seguritan, V. / Zeth, K. / Schwede, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163 KB | Display | ![]() |
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PDB format | ![]() | 136.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 530.1 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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/peptide | Mass: 3250.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 300 uM [U-13C; U-15N] 2.5D, 50 mM sodium phosphate, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 / Details: Refinement in explicit solvent | ||||||||||||
NMR constraints | NOE constraints total: 462 / NOE long range total count: 136 / NOE medium range total count: 78 / Disulfide bond constraints total count: 18 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 15 / Protein psi angle constraints total count: 17 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.33 Å / Torsion angle constraint violation method: CYANA |