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- PDB-3kk1: HIV-1 reverse transcriptase-DNA complex with nuceotide inhibitor ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kk1 | ||||||
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Title | HIV-1 reverse transcriptase-DNA complex with nuceotide inhibitor GS-9148-diphosphate bound in nucleotide site | ||||||
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![]() | TRANSFERASE/DNA / HIV / reverse transcriptase / protein-DNA complex / TRANSFERASE-DNA complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Lansdon, E.B. | ||||||
![]() | ![]() Title: Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex. Authors: Lansdon, E.B. / Samuel, D. / Lagpacan, L. / Brendza, K.M. / White, K.L. / Hung, M. / Liu, X. / Boojamra, C.G. / Mackman, R.L. / Cihlar, T. / Ray, A.S. / McGrath, M.E. / Swaminathan, 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 | ![]() | 239.5 KB | Display | ![]() |
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PDB format | ![]() | 185.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.9 KB | Display | ![]() |
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Full document | ![]() | 824.1 KB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kjvSC ![]() 3kk2C ![]() 3kk3C 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
-Reverse transcriptase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 64521.895 Da / Num. of mol.: 1 / Mutation: C280S, Q258C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 52748.418 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules PT
#3: DNA chain | Mass: 6360.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer DNA |
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#4: DNA chain | Mass: 8423.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template DNA |
-Non-polymers , 4 types, 160 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/914.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/914.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-914 / [( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 3% PEG4000, 0.05M MES pH 6.0, 5mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2008 |
Radiation | Monochromator: double crystal, Si(111) / 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. obs: 39417 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 49.7 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KJV Resolution: 2.7→29.71 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 71802.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.9362 Å2 / ksol: 0.300785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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