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Yorodumi- PDB-5jl4: Inhibitor resistant mutant catalytic core domain of HIV-1 Integrase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jl4 | ||||||
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Title | Inhibitor resistant mutant catalytic core domain of HIV-1 Integrase | ||||||
Components | Integrase | ||||||
Keywords | DNA BINDING PROTEIN / Allini HIV Integrase Multimerization | ||||||
Function / homology | Function and homology information nucleotidyltransferase activity / : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase ...nucleotidyltransferase activity / : / : / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / DNA recombination / nucleic acid binding / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / 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 / MOLECULAR REPLACEMENT / Resolution: 1.758 Å | ||||||
Authors | Feng, L. / Kobe, M. / Kvaratskhelia, M. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Resistance to pyridine-based inhibitor KF116 reveals an unexpected role of integrase in HIV-1 Gag-Pol polyprotein proteolytic processing. Authors: Hoyte, A.C. / Jamin, A.V. / Koneru, P.C. / Kobe, M.J. / Larue, R.C. / Fuchs, J.R. / Engelman, A.N. / Kvaratskhelia, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jl4.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jl4.ent.gz | 101.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/5jl4 ftp://data.pdbj.org/pub/pdb/validation_reports/jl/5jl4 | HTTPS FTP |
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-Related structure data
Related structure data | 1itgS S: Starting model for refinement |
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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: 17951.561 Da / Num. of mol.: 2 / Fragment: UNP residues 50-212 / Mutation: 185K, V165I, T174I 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: D0ENR2, UniProt: P12497*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % |
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Crystal grow | Temperature: 277.5 K / Method: vapor diffusion, hanging drop Details: .2M Ammonium Sulfate 0.1 M BIS-TRIS pH 5.5 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.514 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 1.758→43.037 Å / Num. obs: 29637 / % possible obs: 98.31 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.05641 / Net I/σ(I): 32.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ITG Resolution: 1.758→43.037 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 19.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.758→43.037 Å
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Refine LS restraints |
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LS refinement shell |
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