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- PDB-3tkw: Crystal structure of HIV protease model precursor/Darunavir complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tkw | ||||||
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Title | Crystal structure of HIV protease model precursor/Darunavir complex | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR 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 | ![]() ![]() ![]() | ||||||
![]() | Agniswamy, J. / Sayer, J. / Weber, I. / Louis, J. | ||||||
![]() | ![]() Title: Terminal interface conformations modulate dimer stability prior to amino terminal autoprocessing of HIV-1 protease. Authors: Agniswamy, J. / Sayer, J.M. / Weber, I.T. / Louis, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.2 KB | Display | ![]() |
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PDB format | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tkgC ![]() 3tl9C ![]() 2ienS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11236.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P03367, UniProt: P03366*PLUS, HIV-1 retropepsin |
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-Non-polymers , 5 types, 140 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/017.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/017.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-017 / ( | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.6M Sodium Chloride, 0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. all: 34602 / Num. obs: 34602 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.9 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IEN Resolution: 1.55→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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