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Yorodumi- PDB-8u6d: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
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-Basic information
Entry | Database: PDB / ID: 8u6d | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with N-(2-(4-chloro-3-(3-chloro-5-cyanophenoxy)phenoxy)ethyl)-N-methylacrylamide (JLJ736), a non-nucleoside inhibitor | ||||||
Components |
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Keywords | VIRAL PROTEIN/Inhibitor / REVERSE TRANSCRIPTASE / ANTIVIRAL / DRUG DESIGN / HIV-1 / VIRAL PROTEIN / VIRAL PROTEIN-Inhibitor complex | ||||||
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 / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / 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: 2.33 Å | ||||||
Authors | Hollander, K. / 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 | 8u6d.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u6d.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 8u6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/8u6d ftp://data.pdbj.org/pub/pdb/validation_reports/u6/8u6d | HTTPS FTP |
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-Related structure data
Related structure data | 8u69C 8u6aC 8u6bC 8u6cC 8u6eC 8u6fC 8u6gC 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: 63989.238 Da / Num. of mol.: 1 / Mutation: C879S, K172A, K173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / 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-VTS / |
#4: 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: 2.83 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 50 mM MES pH 5.0, 20% PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine PH range: 5.0-7.5 |
-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: Jul 22, 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: 2.33→80.06 Å / Num. obs: 54256 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.043 / Rrim(I) all: 0.115 / Χ2: 1 / Net I/σ(I): 10.8 / Num. measured all: 380742 |
Reflection shell | Resolution: 2.33→2.46 Å / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.786 / Num. measured all: 57590 / Num. unique obs: 7868 / CC1/2: 0.488 / Rpim(I) all: 0.706 / Rrim(I) all: 1.922 / Χ2: 0.92 / Net I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→35.22 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.87 / 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: 2.33→35.22 Å
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Refine LS restraints |
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LS refinement shell |
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