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Yorodumi- PDB-2vg5: Crystal structures of HIV-1 reverse transcriptase complexes with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vg5 | ||||||
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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 / structural molecule activity / host cell plasma membrane / virion membrane / 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: 2.8 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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vg5.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vg5.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/2vg5 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/2vg5 | 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-NNC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 61.9 % / 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: 31949 / % possible obs: 89.8 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.08 |
-Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.854 / SU B: 16.484 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / 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: 45.11 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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