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- PDB-7otn: HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND INHIBITOR RMC-247 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7otn | ||||||
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Title | HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND INHIBITOR RMC-247 | ||||||
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![]() | TRANSFERASE / REVERSE TRANSCRIPTASE / RT INHIBITOR COMPLEX / ACYCLIC NUCLEOSIDE PHOSPHONATE ANALOG / RT-DNA COMPLEX | ||||||
Function / homology | ![]() HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / 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 / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Martinez, S.E. / Singh, A.K. / Gu, W. / Das, K. | ||||||
![]() | ![]() Title: Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design. Authors: Gu, W. / Martinez, S. / Singh, A.K. / Nguyen, H. / Rozenski, J. / Schols, D. / Herdewijn, P. / Das, K. / De Jonghe, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 457.8 KB | Display | ![]() |
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PDB format | ![]() | 362.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ot6C ![]() 7otaC ![]() 7otkC ![]() 7otxC ![]() 7otzC ![]() 7outC ![]() 3v4iS C: citing same article ( S: Starting model for refinement |
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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
-Reverse transcriptase/ribonuclease ... , 2 types, 4 molecules CADB
#1: Protein | Mass: 64022.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H #2: Protein | Mass: 50039.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Production host: ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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-DNA chain , 2 types, 4 molecules ETFP
#3: DNA chain | Mass: 8383.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 6474.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 5 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/1IH.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 16-19% V/V PEG SMEAR BROAD, 0.2 M (NH4)2SO4, 0.1 M TRIS-HCL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→95.23 Å / Num. obs: 44271 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 113.35 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.082 / Rrim(I) all: 0.206 / Net I/σ(I): 7.3 / Num. measured all: 278514 / Scaling rejects: 746 |
Reflection shell | Resolution: 3.4→3.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 2.328 / Num. unique obs: 4613 / CC1/2: 0.35 / Rpim(I) all: 0.988 / Rrim(I) all: 2.534 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3V4I Resolution: 3.4→95.23 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.11 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 303.63 Å2 / Biso mean: 133.8553 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→95.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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