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- PDB-8stv: Crystal Structure of HIV-1 Reverse Transcriptase (Y181C, V106A) v... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8stv | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase (Y181C, V106A) variant in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-2-naphthonitrile (JLJ600), a non-nucleoside inhibitor | ||||||
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![]() | VIRAL PROTEIN / Hydrolase / 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 | ![]() ![]() ![]() | ||||||
![]() | Hollander, K. / Jorgensen, W.L. / Anderson, K.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Exploring novel HIV-1 reverse transcriptase inhibitors with drug-resistant mutants: A double mutant surprise. Authors: Hollander, K. / Chan, A.H. / Frey, K.M. / Hunker, O. / Ippolito, J.A. / Spasov, K.A. / Yeh, Y.J. / Jorgensen, W.L. / Ho, Y.C. / 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 | ![]() | 384 KB | Display | ![]() |
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PDB format | ![]() | 299.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1016.5 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 63.2 KB | Display | |
Data in CIF | ![]() | 86.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8stpC ![]() 8stqC ![]() 8strC ![]() 8stsC ![]() 8sttSC ![]() 8stuC C: citing same article ( S: Starting model for refinement |
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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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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: 64014.309 Da / Num. of mol.: 2 / Mutation: Y181C, V106A, C280S, K172A, K173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P03366 |
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-Non-polymers , 5 types, 78 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/3LQ.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/3LQ.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #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: 3.03 Å3/Da / Density % sol: 59.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM MES pH 6.0, 16% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine PH range: 6.0-7.5 |
-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: Oct 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→110.58 Å / Num. obs: 69299 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.96 / Net I/σ(I): 12.7 / Num. measured all: 484920 |
Reflection shell | Resolution: 2.78→2.93 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.599 / Num. measured all: 69418 / Num. unique obs: 10068 / CC1/2: 0.459 / Rpim(I) all: 0.656 / Rrim(I) all: 1.731 / Χ2: 0.89 / Net I/σ(I) obs: 1.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8STT Resolution: 2.78→37.83 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.51 / Stereochemistry target values: ML
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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: 2.78→37.83 Å
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Refine LS restraints |
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LS refinement shell |
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