[English] 日本語
![](img/lk-miru.gif)
- PDB-3i0s: crystal structure of HIV reverse transcriptase in complex with in... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3i0s | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of HIV reverse transcriptase in complex with inhibitor 7 | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / HIV-1 reverse transcriptase / non-nucleoside inhibition / nucleotidyltrasferase / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Cell membrane / Cytoplasm / DNA integration / DNA recombination / DNA-directed DNA polymerase / Endonuclease / Host-virus interaction / Hydrolase / Lipoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Myristate / Nuclease / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribosomal frameshifting / RNA-binding / RNA-directed DNA polymerase / Viral nucleoprotein / Virion / Zinc / Zinc-finger | ||||||
Function / homology | ![]() integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yan, Y. / Prasad, S. | ||||||
![]() | ![]() Title: Substituted tetrahydroquinolines as potent allosteric inhibitors of reverse transcriptase and its key mutants. Authors: Su, D.S. / Lim, J.J. / Tinney, E. / Wan, B.L. / Young, M.B. / Anderson, K.D. / Rudd, D. / Munshi, V. / Bahnck, C. / Felock, P.J. / Lu, M. / Lai, M.T. / Touch, S. / Moyer, G. / Distefano, D.J. ...Authors: Su, D.S. / Lim, J.J. / Tinney, E. / Wan, B.L. / Young, M.B. / Anderson, K.D. / Rudd, D. / Munshi, V. / Bahnck, C. / Felock, P.J. / Lu, M. / Lai, M.T. / Touch, S. / Moyer, G. / Distefano, D.J. / Flynn, J.A. / Liang, Y. / Sanchez, R. / Prasad, S. / Yan, Y. / Perlow-Poehnelt, R. / Torrent, M. / Miller, M. / Vacca, J.P. / Williams, T.M. / Anthony, N.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 206.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 163.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 863.1 KB | Display | |
Data in XML | ![]() | 43.6 KB | Display | |
Data in CIF | ![]() | 57.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i0rC ![]() 2rf2S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 64895.316 Da / Num. of mol.: 1 / Fragment: Gag-Pol polyprotein P66 subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
---|---|
#2: Protein | Mass: 51731.418 Da / Num. of mol.: 1 / Fragment: Gag-Pol polyprotein P51 subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04585, RNA-directed DNA polymerase, DNA-directed DNA polymerase |
#3: Chemical | ChemComp-RT7 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.19 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 40026 / Num. obs: 39946 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3961 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2RF2 Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.184 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.719 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.194 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
|