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- PDB-6vy8: NMR solution structure of a triazole bridged trypsin inhibitor ba... -

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Basic information

Entry
Database: PDB / ID: 6vy8
TitleNMR solution structure of a triazole bridged trypsin inhibitor based on the framework of SFTI-1
ComponentsTrypsin inhibitor GLY-ARG-RVJ-THR-LYS-SER-ILE-PRO-PRO-ILE-2AG-PHE-PRO-ASP
KeywordsBIOSYNTHETIC PROTEIN / Triazole / Disulfide mimetic / Inhibitor
Function / homologynegative 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 speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / simulated annealing
AuthorsWhite, A.M. / Harvey, P.J. / Durek, T. / Craik, D.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150100443 Australia
CitationJournal: 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
DepositionFeb 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin inhibitor GLY-ARG-RVJ-THR-LYS-SER-ILE-PRO-PRO-ILE-2AG-PHE-PRO-ASP


Theoretical massNumber of molelcules
Total (without water)1,5431
Polymers1,5431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Trypsin inhibitor GLY-ARG-RVJ-THR-LYS-SER-ILE-PRO-PRO-ILE-2AG-PHE-PRO-ASP


Type: Polypeptide / Class: Trypsin inhibitor / Mass: 1542.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: cyclic trypsin inhibitor, UniProt: Q4GWU5*PLUS
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-1H E.COSY

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Sample preparation

DetailsType: solution / Contents: 1.5 mM DR10, 90% H2O/10% D2O / Label: DR9 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: DR10 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: NA Not defined / Label: H2O/D2O(9:1) and D2O (99.9%) / pH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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