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Yorodumi- PDB-3qip: Structure of HIV-1 reverse transcriptase in complex with an RNase... -
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-Basic information
Entry | Database: PDB / ID: 3qip | ||||||
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Title | Structure of HIV-1 reverse transcriptase in complex with an RNase H inhibitor and nevirapine | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / HIV / reverse transcriptase / RNase H / polymerase / nuclease / TRANSFERASE-TRANSFERASE 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 / 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 / Assembly Of The HIV Virion / HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / peptidase activity / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 | HIV-1 M:B_HXB2R (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0926 Å | ||||||
Authors | Lansdon, E.B. / Kirschberg, T.A. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2011 Title: Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors. Authors: Lansdon, E.B. / Liu, Q. / Leavitt, S.A. / Balakrishnan, M. / Perry, J.K. / Lancaster-Moyer, C. / Kutty, N. / Liu, X. / Squires, N.H. / Watkins, W.J. / Kirschberg, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qip.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qip.ent.gz | 172.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qip_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3qip_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3qip_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 3qip_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/3qip ftp://data.pdbj.org/pub/pdb/validation_reports/qi/3qip | HTTPS FTP |
-Related structure data
Related structure data | 3qinC 3qioC 1vrtS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 64562.949 Da / Num. of mol.: 1 / Fragment: p66 subunit (UNP residues 588-1147) Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Gene: gag-pol / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: p51 subunit (UNP Residues 588-1027) Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Gene: gag-pol / Plasmid: pET 14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P04585, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
-Non-polymers , 6 types, 426 molecules
#3: Chemical | ChemComp-NVP / | ||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-P4Y / | #8: 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: 59.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.3M (NH4)2SO4, 5mM sodium malonate, and 100mM cacodylate pH 6.5, 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: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2007 |
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.0926→50 Å / Num. obs: 82059 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.0926→2.14 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VRT Resolution: 2.0926→47.354 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.512 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.0926→47.354 Å
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Refine LS restraints |
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LS refinement shell |
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