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Yorodumi- PDB-6vy8: NMR solution structure of a triazole bridged trypsin inhibitor ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vy8 | |||||||||
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Title | NMR solution structure of a triazole bridged trypsin inhibitor based on the framework of SFTI-1 | |||||||||
Components | Trypsin inhibitor GLY-ARG-RVJ-THR-LYS-SER-ILE-PRO-PRO-ILE-2AG-PHE-PRO-ASP | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Triazole / Disulfide mimetic / Inhibitor | |||||||||
Function / homology | negative regulation of endopeptidase activity / endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / protease binding / cyclic trypsin inhibitor / Trypsin inhibitor 1 Function and homology information | |||||||||
Biological species | Helianthus annuus (common sunflower) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | White, A.M. / Harvey, P.J. / Durek, T. / Craik, D.J. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides. Authors: White, A.M. / de Veer, S.J. / Wu, G. / Harvey, P.J. / Yap, K. / King, G.J. / Swedberg, J.E. / Wang, C.K. / Law, R.H.P. / Durek, T. / Craik, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vy8.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vy8.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 6vy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vy8_validation.pdf.gz | 375.7 KB | Display | wwPDB validaton report |
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Full document | 6vy8_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 6vy8_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 6vy8_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/6vy8 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/6vy8 | HTTPS FTP |
-Related structure data
Related structure data | 6q1uC 6u22C 6u24C 6u7qC 6u7rC 6u7sC 6u7uC 6u7wC 6u7xC 6vxyC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 1.5 mM DR10, 90% H2O/10% D2O / Label: DR9 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 1.5 mM / Component: DR10 / Isotopic labeling: natural abundance |
Sample conditions | Ionic strength: NA Not defined / Label: H2O/D2O(9:1) and D2O (99.9%) / pH: 3.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |