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- PDB-2vg5: Crystal structures of HIV-1 reverse transcriptase complexes with ... -
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Open data
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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 | ||||||
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![]() | 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 | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Spallarossa, A. / Cesarini, S. / Ranise, A. / Ponassi, M. / Unge, T. / Bolognesi, M. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.3 KB | Display | ![]() |
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PDB format | ![]() | 163.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 855.1 KB | Display | ![]() |
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Full document | ![]() | 920.4 KB | Display | |
Data in XML | ![]() | 44 KB | Display | |
Data in CIF | ![]() | 58.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-NNC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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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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