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- PDB-6r28: Structure of peptide P7, which binds Cdc42 and inhibits effector ... -

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Basic information

Entry
Database: PDB / ID: 6r28
TitleStructure of peptide P7, which binds Cdc42 and inhibits effector interactions.
Componentspeptide P7
KeywordsDE NOVO PROTEIN / Inhibitor / cyclic peptide / synthetic peptide.
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMurphy, N.P. / Mott, H.R. / Owen, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K017101/1 United Kingdom
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The discovery and maturation of peptide biologics targeting the small G-protein Cdc42: A bioblockade for Ras-driven signaling.
Authors: Tetley, G.J.N. / Murphy, N.P. / Bonetto, S. / Ivanova-Berndt, G. / Revell, J. / Mott, H.R. / Cooley, R.N. / Owen, D.
History
DepositionMar 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Sep 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Mar 6, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: peptide P7


Theoretical massNumber of molelcules
Total (without water)2,0701
Polymers2,0701
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide peptide P7


Mass: 2070.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1TOCSY
121isotropic1COSY
131isotropic1NOESY

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Sample preparation

DetailsType: solution / Contents: 5 mg/mL peptide, 90% H2O/10% D2O / Details: 50mM sodium phosphate pH 7.0 / Label: unlabelled sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 5 mg/mL / Component: peptide / Isotopic labeling: none
Sample conditionsIonic strength: 50 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2CCPNchemical shift assignment
ARIA1.2Linge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 35

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