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- PDB-1uts: Designed HIV-1 TAR Binding Ligand -

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Basic information

Entry
Database: PDB / ID: 1uts
TitleDesigned HIV-1 TAR Binding Ligand
ComponentsRNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3')
KeywordsHIV-1 / TAR RNA / DRUG DESIGN / ANTIVIRAL / LIGAND BINDING / CONFORMATIONAL CHANGE
Function / homologyChem-P13 / RNA / RNA (> 10)
Function and homology information
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodSOLUTION NMR / NOE-RESTRAINED DYNAMICS
AuthorsDavis, B. / Murchie, A.I.H. / Aboul-Ela, F. / Karn, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.
Authors: Murchie, A.I. / Davis, B. / Isel, C. / Afshar, M. / Drysdale, M.J. / Bower, J. / Potter, A.J. / Starkey, I.D. / Swarbrick, T.M. / Mirza, S. / Prescott, C.D. / Vaglio, P. / Aboul-ela, F. / Karn, J.
History
DepositionDec 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 5, 2021Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / pdbx_database_status / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
B: RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7152
Polymers9,3081
Non-polymers4081
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 50LEAST RESTRAINT VIOLATION ENERGY
RepresentativeModel #1

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Components

#1: RNA chain RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3') / HIV-1 TAR RNA


Mass: 9307.555 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 29 NUCLEOTIDE SEQUENCE COMPRISING PRIMARY BINDING SITE OF HIV-1 TAT, SYNTHESIZED USING T7 RNA POLYMERASE OFF OF A DNA TEMPLATE
Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS 1
#2: Chemical ChemComp-P13 / N-[2-(3-AMINOPROPOXY)-5-(1H-INDOL-5-YL)BENZYL]-N-(2-PIPERAZIN-1-YLETHYL)AMINE / RBT550 INHIBITOR


Mass: 407.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33N5O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121(H)CCH-TOCSY
131(H)CCH-COSY
141NOESY-HSQC
151LONG RANGE 15N-1H HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED TAR RNA IN D2O AT 303 K, AND UNLABELED TAR RNA IN H2O AT 278 K, ALL COMPLEXED WITH THE SYNTHETIC LIGAND, RBT550

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Sample preparation

Sample conditionsIonic strength: 20 mM / pH: 6.1 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DMXBrukerDMX6003
Bruker AMXBrukerAMX5004

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: NOE-RESTRAINED DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS WERE ACCORDING TO STANDARD METHODS (SEE JOURNAL CITATION ABOVE AND G. VARANI, F. ABOUL-ELA, AND F. ALLAIN, NMR INVESTIGATION OF RNA STRUCTURE. FROM PROGRESS IN NMR ...Details: REFINEMENT DETAILS WERE ACCORDING TO STANDARD METHODS (SEE JOURNAL CITATION ABOVE AND G. VARANI, F. ABOUL-ELA, AND F. ALLAIN, NMR INVESTIGATION OF RNA STRUCTURE. FROM PROGRESS IN NMR SPECTROSCOPY, V. 29, P. 51-127.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 16

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