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Yorodumi- PDB-6ujx: HIV-1 wild-type reverse transcriptase-DNA complex with (-)-FTC-TP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ujx | ||||||
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Title | HIV-1 wild-type reverse transcriptase-DNA complex with (-)-FTC-TP | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 reverse transcriptase NRTI polymerase DNA 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / 2-LTR circle formation / Uncoating of the HIV Virion / 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 / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.70451211695 Å | ||||||
Authors | Lansdon, E.B. | ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: Elucidating molecular interactions ofL-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance. Authors: Hung, M. / Tokarsky, E.J. / Lagpacan, L. / Zhang, L. / Suo, Z. / Lansdon, E.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ujx.cif.gz | 242.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ujx.ent.gz | 182.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ujx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ujx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ujx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ujx_validation.xml.gz | 39 KB | Display | |
Data in CIF | 6ujx_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/6ujx ftp://data.pdbj.org/pub/pdb/validation_reports/uj/6ujx | HTTPS FTP |
-Related structure data
Related structure data | 6uirC 6uisC 6uitC 6ujyC 6ujzC 6uk0C 3kk1S 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 65887.328 Da / Num. of mol.: 1 / Mutation: Q845C,C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 51382.984 Da / Num. of mol.: 1 / Mutation: C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
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#4: DNA chain | Mass: 8448.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
-Non-polymers , 4 types, 118 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-1RY / [[( | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.78 Å3/Da / Density % sol: 55.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2% PEG 4000, MES pH 6.0, 10mM magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97395 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 39743 / % possible obs: 99.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 46.2408981058 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.65→2.7 Å / Rmerge(I) obs: 0.735 / Num. unique obs: 3373 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KK1 Resolution: 2.70451211695→47.5975379997 Å / SU ML: 0.3227080861 / Cross valid method: THROUGHOUT / σ(F): 1.33617033594 / Phase error: 27.3473199799
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.6637549949 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.70451211695→47.5975379997 Å
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Refine LS restraints |
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LS refinement shell |
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