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Yorodumi- PDB-1uud: NMR structure of a synthetic small molecule, rbt203, bound to HIV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uud | ||||||||||||||||||||||
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Title | NMR structure of a synthetic small molecule, rbt203, bound to HIV-1 TAR RNA | ||||||||||||||||||||||
Components | RNA (5'-(*Keywords | HIV-1 / TAR RNA / DRUG DESIGN / LIGAND-RNA INTERACTION / RNA BULGE | Function / homology | Chem-P14 / RNA / RNA (> 10) | Function and homology information Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 | Method | SOLUTION NMR / NOE-RESTRAINED DYNAMICS | Model type details | MINIMIZED AVERAGE | Authors | Davis, B. / Afshar, M. / Varani, G. / Karn, J. / Murchie, A.I.H. / Lentzen, G. / Drysdale, M.J. / Potter, A.J. / Bower, J. / Aboul-Ela, F. | Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Rational Design of Inhibitors of HIV-1 Tar RNA Through the Stabilisation of Electrostatic "Hot Spots" Authors: Davis, B. / Afshar, M. / Varani, G. / Murchie, A.I.H. / Karn, J. / Lentzen, G. / Drysdale, M.J. / Bower, J. / Potter, A.J. / Aboul-Ela, F. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The Structure of the Human Immunodeficiency Virus Recognition by Tat Protein Authors: Aboul-Ela, F. / Jkarn, J. / Varani, G. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uud.cif.gz | 29.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uud.ent.gz | 20 KB | Display | PDB format |
PDBx/mmJSON format | 1uud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uud_validation.pdf.gz | 407.3 KB | Display | wwPDB validaton report |
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Full document | 1uud_full_validation.pdf.gz | 413.9 KB | Display | |
Data in XML | 1uud_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 1uud_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uud ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uud | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | 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 (CLONE 12) |
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#2: Chemical | ChemComp-P14 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB 1995, AS THE NMR SPECTRA FOR THE ...Text: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB 1995, AS THE NMR SPECTRA FOR THE RNA AS ABOUND BY THE LIGAND RBT203 SHOWED SIMILAR NOE AND CHEMICAL SHIFT PATTERNS TO THE LATTER |
-Sample preparation
Sample conditions | Ionic strength: 20 mM / pH: 6.1 / Pressure: 1 atm / Temperature: 298 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: NOE-RESTRAINED DYNAMICS / Software ordinal: 1 Details: REFINEMENT INCLUDED A NUMBER OF MODELLING CONSTRAINTS BASED UPON PREVIOUSLY PUBLISHED DATA, AS WELL AS FINAL GENTLE REFINEMENT STEP USING CHARMM. DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE | |||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRRAINT VIOLATION ENERGY Conformers calculated total number: 50 / Conformers submitted total number: 1 |