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Yorodumi- PDB-7snp: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7snp | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with (E)-3-(3-chloro-5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)-4-(2-morpholinoethoxy)phenoxy)phenyl)acrylonitrile (JLJ530) | ||||||
Components |
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Keywords | HYDROLASE / Transferase/Viral Protein / POLYMERASE / TRANSFERASE / RNASEH / Transferase-Viral Protein 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 type 1 Human immunodeficiency virus type 1 group M subtype B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Frey, K.M. / Anderson, K.S. | ||||||
Funding support | United States, 1items
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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 | 7snp.cif.gz | 215.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7snp.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 7snp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/7snp ftp://data.pdbj.org/pub/pdb/validation_reports/sn/7snp | HTTPS FTP |
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-Related structure data
Related structure data | 7snzC 7so1C 7so2C 7so3C 7so4C 7so6C 4h4mS 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
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03366 |
#3: Chemical | ChemComp-9UV / ( |
#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: 3.41 Å3/Da / Density % sol: 63.91 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, and 50 mM citric acid, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2012 / Details: MONOCHROMATOR |
Radiation | Monochromator: CRYOGENICALLY COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMETER WITH REMARK 200 HORIZONTAL FOCUSING SAGITTAL REMARK 200 BEND SECOND MONO CRYSTAL WITH 4: REMARK 200 1 MAGNIFICATION RATIO ...Monochromator: CRYOGENICALLY COOLED DOUBLE REMARK 200 CRYSTAL MONOCHROMETER WITH REMARK 200 HORIZONTAL FOCUSING SAGITTAL REMARK 200 BEND SECOND MONO CRYSTAL WITH 4: REMARK 200 1 MAGNIFICATION RATIO AND REMARK 200 VERTICALLY FOCUSING MIRROR. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→36.597 Å / Num. obs: 34585 / % possible obs: 99.43 % / Redundancy: 3.8 % / Biso Wilson estimate: 83.81 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.89→2.95 Å / Num. unique obs: 1642 / Rrim(I) all: 0.588 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H4M Resolution: 2.89→36.597 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.23 / Stereochemistry target values: ML
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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 max: 292.22 Å2 / Biso mean: 61.86 Å2 / Biso min: 0.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.42 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.89→36.597 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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