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- PDB-8u6t: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u6t | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(2-(2-(3-acryloyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)ethoxy)phenoxy)-2-naphthonitrile (JLJ758), a non-nucleoside inhibitor | ||||||
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![]() | VIRAL PROTEIN / REVERSE TRANSCRIPTASE / ANTIVIRAL / DRUG DESIGN / HIV-1 | ||||||
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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prucha, G. / Henry, S. / Jorgensen, W.L. / Anderson, K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase. Authors: Prucha, G.R. / Henry, S. / Hollander, K. / Carter, Z.J. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.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 | ![]() | 207.2 KB | Display | ![]() |
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PDB format | ![]() | 159.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 984.1 KB | Display | ![]() |
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Full document | ![]() | 1001.9 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u69C ![]() 8u6aC ![]() 8u6bC ![]() 8u6cC ![]() 8u6dC ![]() 8u6eC ![]() 8u6fC ![]() 8u6gC ![]() 8u6hC ![]() 8u6iC ![]() 8u6jC ![]() 8u6kC ![]() 8u6lC ![]() 8u6mC ![]() 8u6nC ![]() 8u6oC ![]() 8u6pC ![]() 8u6qC ![]() 8u6rC ![]() 8u6sC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 63932.180 Da / Num. of mol.: 1 / Mutation: C879S, K172A, K173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 41 molecules ![](data/chem/img/VO8.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-VO8 / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM MES pH 5.5, 17.5% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine PH range: 5.5-7.8 |
-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: Jul 14, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.248→98.148 Å / Num. obs: 69127 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 58.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.062 / Rrim(I) all: 0.099 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.248→2.287 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.986 / Num. unique obs: 3386 / CC1/2: 0.34 / Rpim(I) all: 1.589 / Rrim(I) all: 2.552 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→36.98 Å
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Refine LS restraints |
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LS refinement shell |
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