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- PDB-3isn: Crystal structure of HIV-1 RT bound to A 6-vinylpyrimidine inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 3isn | ||||||
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Title | Crystal structure of HIV-1 RT bound to A 6-vinylpyrimidine inhibitor | ||||||
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![]() | TRANSFERASE / HYDROLASE / HIV-1 / inhibitor / RT | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ennifar, E. / Freisz, S. / Bec, G. / Dumas, P. / Botta, M. / Radi, M. | ||||||
![]() | ![]() Title: Crystal Structure of HIV-1 Reverse Transcriptase Bound to a Non-Nucleoside Inhibitor with a Novel Mechanism of Action Authors: Freisz, S. / Bec, G. / Radi, M. / Wolff, P. / Crespan, E. / Angeli, L. / Dumas, P. / Maga, G. / Botta, M. / Ennifar, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.9 KB | Display | ![]() |
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PDB format | ![]() | 169.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.1 KB | Display | ![]() |
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Full document | ![]() | 510.2 KB | Display | |
Data in XML | ![]() | 42.1 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ithC ![]() 1dloS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 64516.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 49927.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-EDM / |
#4: Water | ChemComp-HOH / |
Sequence details | E465Q IS MUTAGENESI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM Bis-Tris , 25% PEG 3350, 200mM ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2008 / Details: crystal |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2824 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 49675 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 52.08 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.062 / Net I/σ(I): 26.49 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.53 / Num. unique all: 40894 / Rsym value: 0.737 / % possible all: 67.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1DLO Resolution: 2.5→49.102 Å / FOM work R set: 0.704 / SU ML: 0.41 / σ(F): 0 / σ(I): 0 / Phase error: 35.05 / 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 / Bsol: 50 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.84 Å2 / Biso mean: 63.51 Å2 / Biso min: 25.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→49.102 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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