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Yorodumi- PDB-3c6t: Crystal Structure of HIV Reverse Transcriptase in complex with in... -
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-Basic information
Entry | Database: PDB / ID: 3c6t | ||||||
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Title | Crystal Structure of HIV Reverse Transcriptase in complex with inhibitor 14 | ||||||
Components | (Reverse transcriptase) x 2 | ||||||
Keywords | TRANSFERASE / HIV-1 reverse transcriptase / non-nucleoside inhibition / nucleotidyltrasferase / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Hydrolase / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / RNA-binding / RNA-directed DNA polymerase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | HIV-1 M:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||
Authors | Yan, Y. / Prasad, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: The design and synthesis of diaryl ether second generation HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) with enhanced potency versus key clinical mutations. Authors: Tucker, T.J. / Saggar, S. / Sisko, J.T. / Tynebor, R.M. / Williams, T.M. / Felock, P.J. / Flynn, J.A. / Lai, M.T. / Liang, Y. / McGaughey, G. / Liu, M. / Miller, M. / Moyer, G. / Munshi, V. ...Authors: Tucker, T.J. / Saggar, S. / Sisko, J.T. / Tynebor, R.M. / Williams, T.M. / Felock, P.J. / Flynn, J.A. / Lai, M.T. / Liang, Y. / McGaughey, G. / Liu, M. / Miller, M. / Moyer, G. / Munshi, V. / Perlow-Poehnelt, R. / Prasad, S. / Sanchez, R. / Torrent, M. / Vacca, J.P. / Wan, B.L. / Yan, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c6t.cif.gz | 215.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c6t.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 3c6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c6t_validation.pdf.gz | 789.1 KB | Display | wwPDB validaton report |
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Full document | 3c6t_full_validation.pdf.gz | 831.3 KB | Display | |
Data in XML | 3c6t_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 3c6t_validation.cif.gz | 61.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/3c6t ftp://data.pdbj.org/pub/pdb/validation_reports/c6/3c6t | HTTPS FTP |
-Related structure data
Related structure data | 3c6uC 2rf2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64895.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 isolate / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
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#2: Protein | Mass: 51731.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: HXB2 isolate / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04585 |
#3: Chemical | ChemComp-M14 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: Sodium Citrate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 39565 / Num. obs: 36954 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.103 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.785 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2RF2 Resolution: 2.7→47.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.915 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 1.293 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.378 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→47.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.768 Å / Total num. of bins used: 20
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