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- PDB-1sdt: Crystal structures of HIV protease V82A and L90M mutants reveal c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sdt | ||||||
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Title | Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir binding site. | ||||||
![]() | protease RETROPEPSIN | ||||||
![]() | HYDROLASE / Drug resistance / HIV-1 | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Mahalingam, B. / Wang, Y.-F. / Boross, P.I. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T. | ||||||
![]() | ![]() Title: Crystal structures of HIV protease V82A and L90M mutants reveal changes in the indinavir-binding site Authors: Mahalingam, B. / Wang, Y.-F. / Boross, P.I. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.6 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764 KB | Display | ![]() |
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Full document | ![]() | 765.7 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sduC ![]() 1sdvC ![]() 1dazS 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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1 |
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Unit cell |
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Details | Subunits A and B form a homodimer in the asymmetric unit |
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Components
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: complexed with indinavir / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MK1 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Citrate/phosphate buffer, NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2002 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→33 Å / Num. all: 54269 / Num. obs: 53068 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.3→1.33 Å / % possible all: 87.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAZ Resolution: 1.3→10 Å / Num. parameters: 15911 / Num. restraintsaints: 19915 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 1635 / Occupancy sum non hydrogen: 1728 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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