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Yorodumi- PDB-5oi8: Dissociation of biochemical and antiretroviral activities of Inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oi8 | ||||||
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Title | Dissociation of biochemical and antiretroviral activities of Integrase-LEDGF Allosteric Inhibitors revealed by resistance of A125 polymorphic HIV-1 | ||||||
Components | Pol protein | ||||||
Keywords | VIRAL PROTEIN / HIV-1 / Integrase / Catalytic core domain | ||||||
Function / homology | Function and homology information nucleotidyltransferase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...nucleotidyltransferase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / endonuclease activity / DNA recombination / nucleic acid binding / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ruff, M. / Benarous, R. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration. Authors: Bonnard, D. / Le Rouzic, E. / Eiler, S. / Amadori, C. / Orlov, I. / Bruneau, J.M. / Brias, J. / Barbion, J. / Chevreuil, F. / Spehner, D. / Chasset, S. / Ledoussal, B. / Moreau, F. / Saib, A. ...Authors: Bonnard, D. / Le Rouzic, E. / Eiler, S. / Amadori, C. / Orlov, I. / Bruneau, J.M. / Brias, J. / Barbion, J. / Chevreuil, F. / Spehner, D. / Chasset, S. / Ledoussal, B. / Moreau, F. / Saib, A. / Klaholz, B.P. / Emiliani, S. / Ruff, M. / Zamborlini, A. / Benarous, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oi8.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oi8.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 5oi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oi8_validation.pdf.gz | 888.6 KB | Display | wwPDB validaton report |
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Full document | 5oi8_full_validation.pdf.gz | 889.2 KB | Display | |
Data in XML | 5oi8_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5oi8_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oi8 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oi8 | HTTPS FTP |
-Related structure data
Related structure data | 5oi2C 5oi3C 5oi5C 5oiaC 4lh4S S: Starting model for refinement C: citing same article (ref.) |
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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: 20079.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: I0BY59, UniProt: P03366*PLUS |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-9VN / ( |
#4: Chemical | ChemComp-SO4 / |
#5: 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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Ammonium sulfate, cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 25, 2016 |
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→62.93 Å / Num. obs: 13944 / % possible obs: 99 % / Redundancy: 4.8 % / Net I/σ(I): 28.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LH4 Resolution: 2.35→62.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.98 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.219 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.248 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→62.93 Å
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Refine LS restraints |
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