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Yorodumi- PDB-8u6g: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
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-Basic information
Entry | Database: PDB / ID: 8u6g | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 3-(2-(2-(3-acryloyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-1-yl)ethoxy)-4-chlorophenoxy)-5-chlorobenzonitrile (JLJ744), a non-nucleoside inhibitor | ||||||
Components |
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Keywords | VIRAL PROTEIN / REVERSE TRANSCRIPTASE / ANTIVIRAL / DRUG DESIGN / HIV-1 | ||||||
Function / homology | Function and homology information : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Prucha, G. / Carter, Z. / Jorgensen, W.L. / Anderson, K.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u6g.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u6g.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 8u6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/8u6g ftp://data.pdbj.org/pub/pdb/validation_reports/u6/8u6g | HTTPS FTP |
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-Related structure data
Related structure data | 8u69C 8u6aC 8u6bC 8u6cC 8u6dC 8u6eC 8u6fC 8u6hC 8u6iC 8u6jC 8u6kC 8u6lC 8u6mC 8u6nC 8u6oC 8u6pC 8u6qC 8u6rC 8u6sC 8u6tC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 63861.102 Da / Num. of mol.: 1 / Mutation: C879S, K172A, K173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) 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 / Mutation: C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366 | ||||
#3: Chemical | ChemComp-VVE / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 50 mM Imidazole pH 6.8, 14% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine PH range: 6.8-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 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: 2.77→99.3 Å / Num. obs: 38419 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.059 / Rrim(I) all: 0.111 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.77→2.823 Å / Rmerge(I) obs: 2.497 / Num. unique obs: 1901 / CC1/2: 0.332 / Rpim(I) all: 1.513 / Rrim(I) all: 2.923 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→99.3 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.927 / SU B: 19.798 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 0.643 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.419 Å2
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Refinement step | Cycle: 1 / Resolution: 2.77→99.3 Å
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