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Yorodumi- PDB-4ztf: Crystal Structure of the Prototype Foamy Virus Intasome with a 2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ztf | ||||||
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Title | Crystal Structure of the Prototype Foamy Virus Intasome with a 2-Pyridinone Aminal Inhibitor | ||||||
Components |
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Keywords | Transferase/DNA/Inhibitor / TRANSFERASE-DNA COMPLEX / 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: 2.7 Å | ||||||
Authors | Klein, D.J. / Patel, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Discovery of 2-Pyridinone Aminals: A Prodrug Strategy to Advance a Second Generation of HIV-1 Integrase Strand Transfer Inhibitors. Authors: Raheem, I.T. / Walji, A.M. / Klein, D. / Sanders, J.M. / Powell, D.A. / Abeywickrema, P. / Barbe, G. / Bennet, A. / Clas, S.D. / Dubost, D. / Embrey, M. / Grobler, J. / Hafey, M.J. / ...Authors: Raheem, I.T. / Walji, A.M. / Klein, D. / Sanders, J.M. / Powell, D.A. / Abeywickrema, P. / Barbe, G. / Bennet, A. / Clas, S.D. / Dubost, D. / Embrey, M. / Grobler, J. / Hafey, M.J. / Hartingh, T.J. / Hazuda, D.J. / Miller, M.D. / Moore, K.P. / Pajkovic, N. / Patel, S. / Rada, V. / Rearden, P. / Schreier, J.D. / Sisko, J. / Steele, T.G. / Truchon, J.F. / Wai, J. / 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 | 4ztf.cif.gz | 153.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ztf.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ztf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/4ztf ftp://data.pdbj.org/pub/pdb/validation_reports/zt/4ztf | 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 |
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-DNA chain , 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, 171 molecules
#4: Chemical | ChemComp-ZN / | ||||||||
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#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-X2P / ( | #7: Chemical | #8: Chemical | #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: 3.95 Å3/Da / Density % sol: 68.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | |||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 9, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.7→48.858 Å / Num. obs: 44469 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 84.02 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.5 / Num. measured all: 489046 | |||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0 / % possible all: 100
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-Processing
Software |
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Refinement | Resolution: 2.7→48.858 Å / Cor.coef. Fo:Fc: 0.9355 / Cor.coef. Fo:Fc free: 0.9257 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.199
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Displacement parameters | Biso max: 164.21 Å2 / Biso mean: 71.62 Å2 / Biso min: 35.36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.339 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→48.858 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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