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Yorodumi- PDB-2k2y: Solution structure of the folded domain of intermediate IIIa of T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k2y | ||||||
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Title | Solution structure of the folded domain of intermediate IIIa of Tick Carboxypeptidase Inhibitor | ||||||
Components | Carboxypeptidase inhibitor | ||||||
Keywords | HYDROLASE INHIBITOR / IIIA / Blood coagulation / Fibrinolysis / Metalloenzyme inhibitor / Metalloprotease inhibitor / Secreted | ||||||
Function / homology | Function and homology information acquisition of nutrients from host / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / blood coagulation / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Rhipicephalus bursa (arthropod) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Pantoja-Uceda, D. / Blanco, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The NMR structures of the major intermediates of the two-domain tick carboxypeptidase inhibitor reveal symmetry in its folding and unfolding pathways. Authors: Arolas, J.L. / Pantoja-Uceda, D. / Ventura, S. / Blanco, F.J. / Aviles, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k2y.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k2y.ent.gz | 175 KB | Display | PDB format |
PDBx/mmJSON format | 2k2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k2y_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 2k2y_full_validation.pdf.gz | 550.9 KB | Display | |
Data in XML | 2k2y_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 2k2y_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/2k2y ftp://data.pdbj.org/pub/pdb/validation_reports/k2/2k2y | HTTPS FTP |
-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/peptide | Mass: 4060.591 Da / Num. of mol.: 1 / Fragment: UNP residues 23-61 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EPH2 |
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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: 1.00 mM IIIA, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 1.00 mM / Component: IIIA |
Sample conditions | pH: 3.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: standard CYANA protocol of NOE assignment and structure calculation. The 20 conformers with the lowest final CYANA target function values were subject to restrained energy-minimization in ...Details: standard CYANA protocol of NOE assignment and structure calculation. The 20 conformers with the lowest final CYANA target function values were subject to restrained energy-minimization in explicit water using AMBER 9.0 | |||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |