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- PDB-6c0l: Crystal structure of HIV-1 E138K mutant reverse transcriptase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c0l | ||||||
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Title | Crystal structure of HIV-1 E138K mutant reverse transcriptase in complex with non-nucleoside inhibitor K-5a2 | ||||||
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![]() | REPLICATION / non-nucleoside inhibitor | ||||||
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 / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Y. / Nguyen, L.A. / Smithline, Z.B. / Steitz, T.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors. Authors: Yang, Y. / Kang, D. / Nguyen, L.A. / Smithline, Z.B. / Pannecouque, C. / Zhan, P. / Liu, X. / Steitz, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 448.3 KB | Display | ![]() |
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PDB format | ![]() | 366.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6c0jC ![]() 6c0kC ![]() 6c0nC ![]() 6c0oC ![]() 6c0pC ![]() 6c0rC ![]() 6cgfC ![]() 6dufC ![]() 6dugC ![]() 6duhC ![]() 4g1qS 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() |
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#2: Protein | Mass: 50039.555 Da / Num. of mol.: 1 / Mutation: E138K, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol / Production host: ![]() ![]() |
-Non-polymers , 6 types, 783 molecules ![](data/chem/img/K5A.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-K5A / | ||||
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#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | ChemComp-NA / | ||||
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 50 mM MES buffer (pH 6.0-6.6), 10% (v/v) polyethylene glycol (PEG) 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 10 mM spermine PH range: 6.0-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 91513 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03395 / Rrim(I) all: 0.03945 / Net I/σ(I): 16.53 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.106 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 14549 / CC1/2: 0.483 / Rrim(I) all: 1.286 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G1Q Resolution: 1.95→43.155 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97 / 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: 1.95→43.155 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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