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Yorodumi- PDB-2vg7: Crystal structures of HIV-1 reverse transcriptase complexes with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vg7 | ||||||
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Title | Crystal structures of HIV-1 reverse transcriptase complexes with thiocarbamate non-nucleoside inhibitors | ||||||
Components |
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Keywords | TRANSFERASE / DNA-DIRECTED DNA POLYMERASE / THIOCARBAMATES / PHOSPHORYLATION / DNA INTEGRATION / MAGNESIUM / ZINC-FINGER / RNA-BINDING / LIPOPROTEIN / CORE PROTEIN / ENDONUCLEASE / METAL-BINDING / ZINC / AIDS / HIV-1 / VIRION / NUCLEUS / MEMBRANE / ASPARTYL PROTEASE / CAPSID MATURATION / MULTIFUNCTIONAL ENZYME / RNA-DIRECTED DNA POLYMERASE / REVERSE TRANSCRIPTASE / NUCLEOTIDYLTRANSFERASE / DNA RECOMBINATION / VIRAL NUCLEOPROTEIN / PROTEASE / NUCLEASE / MYRISTATE / HYDROLASE / CYTOPLASM / NON-NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITORS | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | ||||||
Authors | Spallarossa, A. / Cesarini, S. / Ranise, A. / Ponassi, M. / Unge, T. / Bolognesi, M. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: Crystal Structures of HIV-1 Reverse Transcriptase Complexes with Thiocarbamate Non-Nucleoside Inhibitors. Authors: Spallarossa, A. / Cesarini, S. / Ranise, A. / Ponassi, M. / Unge, T. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vg7.cif.gz | 199.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vg7.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vg7 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vg7 | HTTPS FTP |
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-Related 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: 64161.535 Da / Num. of mol.: 1 Fragment: GAG-POL POLYPROTEIN P66 SUBUNIT, RESIDUES 600-1156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 50055.551 Da / Num. of mol.: 1 Fragment: GAG-POL POLYPROTEIN P51 SUBUNIT, RESIDUES 600-1027 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03366 |
#3: Chemical | ChemComp-NNI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 62.84 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.969 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 35517 / % possible obs: 81.1 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→20 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.803 / SU B: 17.52 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.546 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.82→20 Å
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