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- PDB-8u6b: 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: 8u6b | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with N-(4-chloro-3-(3-chloro-5-cyanophenoxy)phenethyl)acrylamide (JLJ731), a non-nucleoside inhibitor | ||||||
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![]() | VIRAL PROTEIN / REVERSE TRANSCRIPTASE / ANTIVIRAL / DRUG DESIGN / HIV-1 | ||||||
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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hollander, K. / 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 | ![]() | 200.8 KB | Display | ![]() |
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PDB format | ![]() | 153.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8u69C ![]() 8u6aC ![]() 8u6cC ![]() 8u6dC ![]() 8u6eC ![]() 8u6fC ![]() 8u6gC ![]() 8u6hC ![]() 8u6iC ![]() 8u6jC ![]() 8u6kC ![]() 8u6lC ![]() 8u6mC ![]() 8u6nC ![]() 8u6oC ![]() 8u6pC ![]() 8u6qC ![]() 8u6rC ![]() 8u6sC ![]() 8u6tC 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
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: C879S, 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 |
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#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-VTN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM MES pH 5.5, 21.5% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine PH range: 5.0-7.0 |
-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: Aug 9, 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: 2.35→106.99 Å / Num. obs: 52318 / % possible obs: 98.3 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.043 / Rrim(I) all: 0.115 / Χ2: 0.86 / Net I/σ(I): 9.5 / Num. measured all: 365297 |
Reflection shell | Resolution: 2.35→2.47 Å / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.637 / Num. measured all: 56100 / Num. unique obs: 7698 / CC1/2: 0.52 / Rpim(I) all: 0.647 / Rrim(I) all: 1.762 / Χ2: 0.72 / Net I/σ(I) obs: 1.2 |
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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: 2.35→79.78 Å
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Refine LS restraints |
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LS refinement shell |
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