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- PDB-5hp1: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA ap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hp1 | |||||||||
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Title | STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A DNA aptamer and FOSCARNET, a Pyrophosphate analog | |||||||||
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![]() | TRANSFERASE/INHIBITOR/DNA / RT / DNA APTAMER / Foscavir / N site complex / pyrophosphate / pyrophosphorolysis / phosphonoformic acid / PFA / 2-O-METHYLCYTIDINE / P51 / P66 / TRANSFERASE / TRANSFERASE-INHIBITOR-DNA complex | |||||||||
Function / homology | ![]() HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / 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 / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Das, K. / Arnold, E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet. Authors: Das, K. / Balzarini, J. / Miller, M.T. / Maguire, A.R. / DeStefano, J.J. / Arnold, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 452.3 KB | Display | ![]() |
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PDB format | ![]() | 358.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 71 KB | Display | |
Data in CIF | ![]() | 94.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hroC ![]() 5i3uC ![]() 5i42C ![]() 5d3gS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-HIV-1 REVERSE TRANSCRIPTASE ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 63875.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Production host: ![]() ![]() #2: Protein | Mass: 51928.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Production host: ![]() ![]() |
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-DNA chain / Sugars , 2 types, 4 molecules FE
#3: DNA chain | Mass: 11748.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Polysaccharide | |
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-Non-polymers , 6 types, 18 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/PPF.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ATM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PPF.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ATM.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 7% PEG 8000, 25mM, BISTRIS-PROPANE, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE PH range: 6.8 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 63660 / % possible obs: 96.7 % / Observed criterion σ(I): -1 / Redundancy: 4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 1.37 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5D3G Resolution: 2.9→45.643 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→45.643 Å
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Refine LS restraints |
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LS refinement shell |
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