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- PDB-6uxs: Solution structure of the cyclic peptide 3.1B -

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Basic information

Entry
Database: PDB / ID: 6uxs
TitleSolution structure of the cyclic peptide 3.1B
ComponentsCyclic peptide 3.1B
KeywordsTRANSCRIPTION / Bromodomain / BET / Cyclic Peptide / Inhibitor / RAPID
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / na
AuthorsSolomon, P.D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1161623 Australia
CitationJournal: To Be Published
Title: Solution structure of the cyclic peptide 3.1B
Authors: Solomon, P.D.
History
DepositionNov 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic peptide 3.1B


Theoretical massNumber of molelcules
Total (without water)1,9161
Polymers1,9161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area160 Å2
ΔGint-2 kcal/mol
Surface area1900 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cyclic peptide 3.1B


Mass: 1916.273 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
141isotropic11D
111isotropic12D COSY
121isotropic12D TOCSY
131isotropic12D NOESY

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Sample preparation

DetailsType: solution
Contents: 835 uM 3.1B, 10 mM Phosphate Buffer, 95% H2O/5% D2O
Details: 10 mM Phosphate Buffer pH 7.2 / Label: unlabelled / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
835 uM3.1Bnatural abundance1
10 mMPhosphate Buffernatural abundance1
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 278 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
CYANA2.98.5Guntert, Mumenthaler and Wuthrichrefinement
CcpNmr AnalysisCCPNpeak picking
CYANA2.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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