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Yorodumi- PDB-7so6: Crystal Structure of HIV-1 K103N, Y181C mutant Reverse Transcript... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7so6 | ||||||||||||
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Title | Crystal Structure of HIV-1 K103N, Y181C mutant Reverse Transcriptase in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-7-fluoro-2-naphthonitrile (JLJ635), a Non-nucleoside Inhibitor | ||||||||||||
Components |
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Keywords | TRANSFERASE / Viral Protein / NNRTIs / HIV-1 / drug design | ||||||||||||
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 type 1 group M subtype B | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||||||||
Authors | Bertoletti, N. / Frey, K.M. / Anderson, K.S. / Cisneros Trigo, J.A. / Jorgensen, W.L. / Chan, A.H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucleoside Inhibitors and Their Interactions With HIV-1 Reverse Transcriptase. Authors: Frey, K.M. / Bertoletti, N. / Chan, A.H. / Ippolito, J.A. / Bollini, M. / 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 | 7so6.cif.gz | 206 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7so6.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 7so6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/7so6 ftp://data.pdbj.org/pub/pdb/validation_reports/so/7so6 | HTTPS FTP |
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-Related structure data
Related structure data | 7snpC 7snzC 7so1C 7so2C 7so3C 7so4C 6oe3S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 63914.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Gene: gag-pol Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P03366, RNA-directed DNA polymerase |
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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.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P03366 |
#3: Chemical | ChemComp-M9A / |
#4: Chemical | ChemComp-MG / |
#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: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0 mM MES pH 6.0, 18% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 31556 / % possible obs: 99.3 % / Redundancy: 3.75 % / Biso Wilson estimate: 74.23 Å2 / CC1/2: 0.995 / CC star: 0.995 / Rrim(I) all: 0.084 / Rsym value: 0.073 / Net I/σ(I): 14.51 |
Reflection shell | Resolution: 2.79→2.87 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.62 / Num. unique obs: 2197 / CC1/2: 0.813 / CC star: 0.813 / Rrim(I) all: 0.672 / Rsym value: 0.571 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OE3 Resolution: 2.79→48.26 Å / SU ML: 0.4484 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 30.8403 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→48.26 Å
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Refine LS restraints |
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LS refinement shell |
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