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- PDB-7so4: Crystal Structure of HIV-1 Y181C mutant Reverse Transcriptase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7so4 | ||||||||||||
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Title | Crystal Structure of HIV-1 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 | ||||||||||||
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![]() | hydrolase / transferase/viral protein / NNRTIs / HIV-1 / drug design / TRANSFERASE / transferase-viral protein complex | ||||||||||||
Function / homology | ![]() 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 ...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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 | ![]() ![]() ![]() | ||||||||||||
![]() | Bertoletti, N. / Anderson, K.S. / Cisneros Trigo, J.A. / Jorgensen, W.L. / Frey, K.M. / Chan, A.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.4 KB | Display | ![]() |
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PDB format | ![]() | 160.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 767.4 KB | Display | ![]() |
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Full document | ![]() | 778.9 KB | Display | |
Data in XML | ![]() | 33 KB | Display | |
Data in CIF | ![]() | 44.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7snpC ![]() 7snzC ![]() 7so1C ![]() 7so2C ![]() 7so3C ![]() 7so6C ![]() 6oe3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 63929.207 Da / Num. of mol.: 1 / Mutation: Y181C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gag-pol Production host: ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease 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.) ![]() Strain: isolate BH10 / Gene: gag-pol Production host: ![]() ![]() References: UniProt: P03366 |
#3: Chemical | ChemComp-M9A / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 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: 2.95→50 Å / Num. obs: 26134 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 82.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.069 / Rsym value: 0.059 / Net I/σ(I): 17.82 |
Reflection shell | Resolution: 2.95→3.12 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.41 / Num. unique obs: 3988 / CC1/2: 0.807 / CC star: 0.807 / Rrim(I) all: 0.74 / Rsym value: 0.63 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OE3 Resolution: 2.95→43.02 Å / SU ML: 0.4479 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 30.9357 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: 89.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→43.02 Å
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Refine LS restraints |
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LS refinement shell |
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