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Yorodumi- PDB-6ul5: Crystal structure of HIV-1 reverse transcriptase (RT) in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ul5 | ||||||
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Title | Crystal structure of HIV-1 reverse transcriptase (RT) in complex with 4-[(4-{4-[(E)-2-cyanoethenyl]-2,6-dimethylphenoxy}thieno[3,2-d]pyrimidin-2-yl)amino]-2-fluorobenzonitrile (24b), a non-nucleoside RT inhibitor | ||||||
Components | (Reverse transcriptase ...) x 2 | ||||||
Keywords | TRANSFERASE / Human immunodeficiency virus 1 / non nucleotide-reverse transcriptase inhibitor | ||||||
Function / homology | Function and homology information symbiont-mediated activation of host apoptosis / 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 ...symbiont-mediated activation of host apoptosis / 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 / 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 / viral translational frameshifting / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Ruiz, F.X. / Pilch, A. / Arnold, E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery and Characterization of Fluorine-Substituted Diarylpyrimidine Derivatives as Novel HIV-1 NNRTIs with Highly Improved Resistance Profiles and Low Activity for the hERG Ion Channel. Authors: Kang, D. / Ruiz, F.X. / Feng, D. / Pilch, A. / Zhao, T. / Wei, F. / Wang, Z. / Sun, Y. / Fang, Z. / De Clercq, E. / Pannecouque, C. / Arnold, E. / Liu, X. / Zhan, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ul5.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ul5.ent.gz | 174.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ul5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ul5_validation.pdf.gz | 350.5 KB | Display | wwPDB validaton report |
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Full document | 6ul5_full_validation.pdf.gz | 350.6 KB | Display | |
Data in XML | 6ul5_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6ul5_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/6ul5 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/6ul5 | HTTPS FTP |
-Related structure data
Related structure data | 4g1qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Reverse transcriptase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K172A, K173A, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 50096.539 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366 |
-Non-polymers , 5 types, 332 molecules
#3: Chemical | ChemComp-QAG / | ||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 10%(v/v) PEG 8000, 4%(v/v) PEG 400, 100 mM MES pH 6.3, 10 mM spermine, 15 mM MgSO4, 100 mM ammonium sulfate, and 5 mM tris(2-carboxyethyl)phosphine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→50 Å / Num. obs: 59921 / % possible obs: 98.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 43.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.042 / Rrim(I) all: 0.131 / Net I/σ(I): 13.32 |
Reflection shell | Resolution: 2.23→2.28 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2520 / CC1/2: 0.221 / Rpim(I) all: 0.461 / Rrim(I) all: 0.759 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G1Q Resolution: 2.23→41.27 Å / SU ML: 0.3256 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.5478
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→41.27 Å
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Refine LS restraints |
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LS refinement shell |
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