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Yorodumi- PDB-2kmo: Solution structure of native Leech-derived tryptase inhibitor, LDTI -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kmo | ||||||
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Title | Solution structure of native Leech-derived tryptase inhibitor, LDTI | ||||||
Components | Leech-derived tryptase inhibitor C | ||||||
Keywords | HYDROLASE / Disulfide bond / Protease inhibitor / Serine protease inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Hirudo medicinalis (medicinal leech) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Pantoja-Uceda, D. / Santoro, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Deciphering the structural basis that guides the oxidative folding of leech-derived tryptase inhibitor. Authors: Pantoja-Uceda, D. / Arolas, J.L. / Aviles, F.X. / Santoro, J. / Ventura, S. / Sommerhoff, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kmo.cif.gz | 243.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kmo.ent.gz | 211.1 KB | Display | PDB format |
PDBx/mmJSON format | 2kmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kmo_validation.pdf.gz | 334.9 KB | Display | wwPDB validaton report |
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Full document | 2kmo_full_validation.pdf.gz | 369.2 KB | Display | |
Data in XML | 2kmo_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 2kmo_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/2kmo ftp://data.pdbj.org/pub/pdb/validation_reports/km/2kmo | HTTPS FTP |
-Related structure data
Related structure data | 2kmpC 2kmqC 2kmrC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4523.353 Da / Num. of mol.: 1 / Fragment: residues 1-44 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Plasmid: pVT102U/a / Production host: Escherichia coli (E. coli) / References: UniProt: P80424 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 1.7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: energy minimization with NMR distance constraints using a generalized Born solvent model | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20 |