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- PDB-6bvw: SFTI-HFRW-3 -

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Basic information

Entry
Database: PDB / ID: 6bvw
TitleSFTI-HFRW-3
ComponentsTrypsin inhibitor 1 HFRW-3
KeywordsBIOSYNTHETIC PROTEIN / melanocortin / pharmacophore / cyclic peptide
Function / homologynegative regulation of endopeptidase activity / endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / protease binding / Trypsin inhibitor 1
Function and homology information
Biological speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSchroeder, C.I.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)DC017037 Australia
CitationJournal: J.Med.Chem. / Year: 2018
Title: Development of Novel Melanocortin Receptor Agonists Based on the Cyclic Peptide Framework of Sunflower Trypsin Inhibitor-1.
Authors: Durek, T. / Cromm, P.M. / White, A.M. / Schroeder, C.I. / Kaas, Q. / Weidmann, J. / Ahmad Fuaad, A. / Cheneval, O. / Harvey, P.J. / Daly, N.L. / Zhou, Y. / Dellsen, A. / Osterlund, T. / ...Authors: Durek, T. / Cromm, P.M. / White, A.M. / Schroeder, C.I. / Kaas, Q. / Weidmann, J. / Ahmad Fuaad, A. / Cheneval, O. / Harvey, P.J. / Daly, N.L. / Zhou, Y. / Dellsen, A. / Osterlund, T. / Larsson, N. / Knerr, L. / Bauer, U. / Kessler, H. / Cai, M. / Hruby, V.J. / Plowright, A.T. / Craik, D.J.
History
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Dec 26, 2018Group: Data collection / Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Jul 3, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.4Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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
Revision 2.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Trypsin inhibitor 1 HFRW-3


Theoretical massNumber of molelcules
Total (without water)1,7171
Polymers1,7171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Trypsin inhibitor 1 HFRW-3


Mass: 1717.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H TOCSY
121anisotropic12D 1H-1H NOESY
131anisotropic12D 1H-13C HSQC
141anisotropic12D 1H-15N HSQC
151anisotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution / Contents: 1 mM protein, 90% H2O/10% D2O / Label: sample 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: protein / Isotopic labeling: natural abundance
Sample conditionsIonic strength units: Not defined / Label: conditions_1 / pH: 3.5 / Pressure: 1 Pa / 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
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
TopSpinBruker Biospinprocessing
CcpNMRCCPNchemical shift calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 24

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