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Yorodumi- PDB-3tam: Crystal structure of HIV-1 reverse transcriptase (K103N mutant) i... -
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-Basic information
Entry | Database: PDB / ID: 3tam | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase (K103N mutant) in complex with inhibitor M06 | ||||||
Components |
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Keywords | Transferase/transferase Inhibitor / HIV-1 reverse transcriptase / non-nucleoside inhibition / nucleotidyltranferase / K103N / HIV-1 / Transferase-transferase Inhibitor complex | ||||||
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 / Assembly Of The HIV Virion / HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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: 2.51 Å | ||||||
Authors | Yan, Y. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Design and synthesis of pyridone inhibitors of non-nucleoside reverse transcriptase. Authors: Gomez, R. / Jolly, S. / Williams, T. / Tucker, T. / Tynebor, R. / Vacca, J. / McGaughey, G. / Lai, M.T. / Felock, P. / Munshi, V. / DeStefano, D. / Touch, S. / Miller, M. / Yan, Y. / ...Authors: Gomez, R. / Jolly, S. / Williams, T. / Tucker, T. / Tynebor, R. / Vacca, J. / McGaughey, G. / Lai, M.T. / Felock, P. / Munshi, V. / DeStefano, D. / Touch, S. / Miller, M. / Yan, Y. / Sanchez, R. / Liang, Y. / Paton, B. / Wan, B.L. / Anthony, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tam.cif.gz | 214.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tam.ent.gz | 169.7 KB | Display | PDB format |
PDBx/mmJSON format | 3tam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tam_validation.pdf.gz | 771.2 KB | Display | wwPDB validaton report |
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Full document | 3tam_full_validation.pdf.gz | 788.5 KB | Display | |
Data in XML | 3tam_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 3tam_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/3tam ftp://data.pdbj.org/pub/pdb/validation_reports/ta/3tam | HTTPS FTP |
-Related structure data
Related structure data | 3lp1S 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: 64880.238 Da / Num. of mol.: 1 / Fragment: unp residues 590-1147 / Mutation: K103N Source method: isolated from a genetically manipulated source Details: p66 RT / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 / Gene: gag-pol, HIV-1 / Production host: Escherichia coli (E. coli) References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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#2: Protein | Mass: 51716.340 Da / Num. of mol.: 1 / Fragment: unp residues 588-1027 / Mutation: K103N Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2 / Gene: gag-pol, HIV-1 / Production host: Escherichia coli (E. coli) References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
#3: Chemical | ChemComp-M06 / |
#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: 3.03 Å3/Da / Density % sol: 59.39 % |
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Crystal grow | Temperature: 298 K / pH: 6.1 Details: sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→50 Å / Num. obs: 42589 / % possible obs: 87.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.83 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 16.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3LP1 Resolution: 2.51→16.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.473 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 62.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→16.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.58 Å / Total num. of bins used: 20
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