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- PDB-6kdm: HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kdm | ||||||
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Title | HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:entecavir 5'-triphosphate ternary complex | ||||||
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![]() | TRANSFERASE/DNA / Entecavir 5'-TRIPHOSPHATE / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / TRANSFERASE-DNA complex / REPLICATION | ||||||
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 / 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: Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine. 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 | ![]() | 893.8 KB | Display | ![]() |
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PDB format | ![]() | 732.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kdjC ![]() 6kdkC ![]() 6kdnC ![]() 6kdoC ![]() 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: 64033.387 Da / Num. of mol.: 2 / Mutation: Y214F, F215Y, Q250M, 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, 488 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ET9.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #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: 2.92 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, 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: Dec 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 125038 / % possible obs: 100 % / Redundancy: 5.4 % / Rrim(I) all: 0.098 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6180 / Rrim(I) all: 0.944 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XN1 Resolution: 2.32→48.672 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→48.672 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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