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- PDB-2ns4: Solution structure of a Beta-Hairpin Peptidomimetic Inhibitor of ... -

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Entry
Database: PDB / ID: 2ns4
TitleSolution structure of a Beta-Hairpin Peptidomimetic Inhibitor of the BIV Tat-Tar Interaction
ComponentsL-22 CYCLIC PEPTIDE
KeywordsRNA BINDING PROTEIN / peptidomimetics / peptide structure / RNA recognition / immunodeficiency virus / TAR RNA
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMoehle, K. / Patora, K. / Robinson, J.A.
CitationJournal: Biochemistry / Year: 2007
Title: Structure-Guided Peptidomimetic Design Leads to Nanomolar beta-Hairpin Inhibitors of the Tat-TAR Interaction of Bovine Immunodeficiency Virus
Authors: Athanassiou, Z. / Patora, K. / Dias, R.L.A. / Moehle, K. / Robinson, J.A. / Varani, G.
History
DepositionNov 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-22 CYCLIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)1,7681
Polymers1,7681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide L-22 CYCLIC PEPTIDE


Mass: 1768.189 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The L-22 peptide was synthesized by solid phase synthesis and purified by reverse phase HPLC.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: unlabeled 5mM L-22 cyclic peptide; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 2.3 / Pressure: 1 atom / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5P.GUNTERT ET AL.refinement
XwinNMR2.6Brukerprocessing
XEASY1.53data analysis
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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