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- PDB-6ika: HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ika | ||||||
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Title | HIV-1 reverse transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:DNA:entecavir-triphosphate ternary complex | ||||||
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![]() | TRANSFERASE/DNA / ENTECAVIR 5'-TRIPHOSPHATE / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / entecavir / TRANSFERASE-DNA complex / REPLICATION | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified ...Title: Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors. Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 888.3 KB | Display | ![]() |
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PDB format | ![]() | 729.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 73.2 KB | Display | |
Data in CIF | ![]() | 98.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ik9C ![]() 5xn1S 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
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 63985.387 Da / Num. of mol.: 2 Mutation: G211S, D212A, Y214F, F215Y, Q250M, I258L, F259L, C261S, C379S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S, C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 1 types, 2 molecules EF
#3: DNA chain | Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 157 molecules ![](data/chem/img/ET9.gif)
![](data/chem/img/GOL.gif)
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![](data/chem/img/HOH.gif)
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#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20 mM Bis-Tris-HCl PH 6.0, 30-40 mM di-ammonium hydrogen citrate, 20 mM MgCl2, 3.5-4% PEG 6000, 2.4% sucrose, 4.8% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.598→50 Å / Num. obs: 89785 / % possible obs: 99.6 % / Redundancy: 5.42 % / CC1/2: 0.998 / Rrim(I) all: 0.091 / Net I/σ(I): 15.89 |
Reflection shell | Resolution: 2.598→2.76 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 14209 / CC1/2: 0.711 / Rrim(I) all: 0.844 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XN1 Resolution: 2.598→48.869 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.598→48.869 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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