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- PDB-2l8h: Chemical probe bound to HIV TAR RNA -

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Basic information

Entry
Database: PDB / ID: 2l8h
TitleChemical probe bound to HIV TAR RNA
ComponentsHIV TAR RNA
KeywordsRNA
Function / homologyARGININE / 4-methoxynaphthalen-2-amine / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsDavidson, A. / Begley, D. / Lau, C. / Varani, G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: A Small-Molecule Probe Induces a Conformation in HIV TAR RNA Capable of Binding Drug-Like Fragments.
Authors: Davidson, A. / Begley, D.W. / Lau, C. / Varani, G.
History
DepositionJan 12, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Feb 15, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV TAR RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6563
Polymers9,3081
Non-polymers3482
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain HIV TAR RNA


Mass: 9307.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription using T7 polymerase / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-L8H / 4-methoxynaphthalen-2-amine


Mass: 173.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: fragment based ligand design for HIV-1 TAR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2111H-1H NOESY
1221H-1H NOESY with WATERGATE
2311H-1H TOCSY
243(H)CCH-COSY
25313C HSQC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM HIV TAR RNA, 4 mM Arginine 4-methoxy-napthylamide, 99.99% D2O99.99% D2O
21 mM HIV TAR RNA, 4 mM Arginine 4-methoxy-napthylamide, 90% H2O, 10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] HIV TAR RNA, 4 mM Arginine 4-methoxy-napthylamide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHIV TAR RNA-11
4 mMArginine 4-methoxy- -napthylamide-21
1 mMHIV TAR RNA-32
4 mMArginine 4-methoxy- -napthylamide-42
1 mMHIV TAR RNA-5[U-100% 13C; U-100% 15N]3
4 mMArginine 4-methoxy- -napthylamide-63
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM potassium phosphate 6.6 ambient 277 K
210 mM potassium phosphate 6.6 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX6002

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Processing

NMR softwareName: X-PLOR / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: RDC restraints applied after initial structure calculations
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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