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Yorodumi- PDB-4i7f: HIV-1 Reverse Transcriptase in complex with a phosphonate analog ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i7f | ||||||
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Title | HIV-1 Reverse Transcriptase in complex with a phosphonate analog of nevirapine | ||||||
Components | (Reverse transcriptase) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / NNRTI / HIV / Reverse Transcriptase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | HIV-1 M:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lansdon, E.B. / Parrish, J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Synthesis and biological evaluation of phosphonate analogues of nevirapine. Authors: Parrish, J. / Tong, L. / Wang, M. / Chen, X. / Lansdon, E.B. / Cannizzaro, C. / Zheng, X. / Desai, M.C. / Xu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i7f.cif.gz | 206.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i7f.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 4i7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/4i7f ftp://data.pdbj.org/pub/pdb/validation_reports/i7/4i7f | HTTPS FTP |
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-Related structure data
Related structure data | 1vrtS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64562.949 Da / Num. of mol.: 1 / Fragment: p66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2D / Gene: gag-pol, reverse transcriptase / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, RNA-directed DNA polymerase |
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: p51 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Strain: HXB2D / Gene: gag-pol, reverse transcriptase / Plasmid: pET 14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04585, RNA-directed DNA polymerase |
-Non-polymers , 5 types, 92 molecules
#3: Chemical | ChemComp-NVE / | ||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MG / | #6: Chemical | #7: 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: 3.04 Å3/Da / Density % sol: 59.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.4M ammonium sulfate, 100mM cacodylate pH 6.5, 50mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2007 |
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 3.6 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VRT Resolution: 2.5→30 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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