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Yorodumi- PDB-5uop: CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2-... -
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-Basic information
Entry | Database: PDB / ID: 5uop | ||||||
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Title | CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 18) | ||||||
Components |
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Keywords | TRANSFERASE/DNA/INHIBITOR / DNA INTEGRATION / VIRAL PROTEIN / RECOMBINATION-INHIBITOR-DNA COMPLEX / TRANSFERASE-DNA-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / 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 ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion component / 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 / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / proteolysis / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Human spumaretrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å | ||||||
Authors | Klein, D.J. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV. Authors: Schreier, J.D. / Embrey, M.W. / Raheem, I.T. / Barbe, G. / Campeau, L.C. / Dubost, D. / McCabe Dunn, J. / Grobler, J. / Hartingh, T.J. / Hazuda, D.J. / Klein, D. / Miller, M.D. / Moore, K.P. ...Authors: Schreier, J.D. / Embrey, M.W. / Raheem, I.T. / Barbe, G. / Campeau, L.C. / Dubost, D. / McCabe Dunn, J. / Grobler, J. / Hartingh, T.J. / Hazuda, D.J. / Klein, D. / Miller, M.D. / Moore, K.P. / Nguyen, N. / Pajkovic, N. / Powell, D.A. / Rada, V. / Sanders, J.M. / Sisko, J. / Steele, T.G. / Wai, J. / Walji, A. / Xu, M. / Coleman, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uop.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uop.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 5uop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/5uop ftp://data.pdbj.org/pub/pdb/validation_reports/uo/5uop | 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44456.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Gene: pol / Production host: Escherichia coli (E. coli) References: UniProt: P14350, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-NUCLEOTIDE PREPROCESSED PFV DONOR DNA ... , 2 types, 2 molecules CD
#2: DNA chain | Mass: 5834.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human spumaretrovirus |
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#3: DNA chain | Mass: 5195.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human spumaretrovirus |
-Non-polymers , 6 types, 193 molecules
#4: Chemical | ChemComp-ZN / | ||||||||
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#5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-8G4 / ( | #9: 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: 3.91 Å3/Da / Density % sol: 68.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.25 M AMMONIUM SULFATE, 25% (V/V)GLYCEROL, 4.8% (V/V) 1,6-HEXANEDIOL, 50 MM MES-NAOH, 1MM EDTA, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.846→159 Å / Num. obs: 37741 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 94.19 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.85→2.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 1.619 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Resolution: 2.85→36.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.217
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Displacement parameters | Biso mean: 78.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→36.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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