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- PDB-8bv2: Biological and structural analysis of new potent Integrase-LEDGF ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bv2 | ||||||
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Title | Biological and structural analysis of new potent Integrase-LEDGF allosteric HIV-1 inhibitors | ||||||
![]() | Integrase | ||||||
![]() | VIRAL PROTEIN / inhibitors / integrase / HIV-1 | ||||||
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 | ![]() ![]() | ||||||
![]() | Ruff, M. / Benarous, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase. Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. ...Authors: Bonnard, D. / Le Rouzic, E. / Singer, M.R. / Yu, Z. / Le Strat, F. / Batisse, C. / Batisse, J. / Amadori, C. / Chasset, S. / Pye, V.E. / Emiliani, S. / Ledoussal, B. / Ruff, M. / Moreau, F. / Cherepanov, P. / Benarous, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 29.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 867.6 KB | Display | ![]() |
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Full document | ![]() | 868.2 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cbrC ![]() 8cbsC ![]() 8cbtC ![]() 8cbuC ![]() 8cbvC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20139.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P12497, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-RWR / ( |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 3 microliters of protein at 5 mg/mL in 50 mM MES pH5.5, 50 mM NaCl, 5 mM DTT mixed with 3 microliters of reservoir solution containing 0.1 M sodium cacodylate pH 6.5, 1.26 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 131582 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 29.84 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0286 / Rpim(I) all: 0.01 / Rrim(I) all: 0.03 / Net I/σ(I): 57.43 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.1985 / Mean I/σ(I) obs: 11.2 / Num. unique obs: 13489 / CC1/2: 0.986 / CC star: 0.997 / Rpim(I) all: 0.06627 / Rrim(I) all: 0.2094 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.97 Å
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Refine LS restraints |
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LS refinement shell |
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