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Open data
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Basic information
Entry | Database: PDB / ID: 3oud | ||||||
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Title | MDR769 HIV-1 protease complexed with CA/p2 hepta-peptide | ||||||
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![]() | HYDROLASE/PEPTIDE / MDR HIV-1 protease / inhibitor / drug resistance / substrate envelope / HIV-1 protease / protease / CA/p2 substrate peptide / none / HYDROLASE / HYDROLASE-PEPTIDE 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 / endonuclease activity / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Kovari, L.C. | ||||||
![]() | ![]() Title: Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease. Authors: Liu, Z. / Wang, Y. / Brunzelle, J. / Kovari, I.A. / Kovari, L.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 41.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.5 KB | Display | ![]() |
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Full document | ![]() | 443.7 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3otsC ![]() 3otyC ![]() 3ou1C ![]() 3ou3C ![]() 3ou4C ![]() 3ouaC ![]() 3oubC ![]() 3oucC 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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1 |
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Unit cell |
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Details | MDR HIV-1 protease dimer binds with CA/p2 substrate peptide |
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Components
#1: Protein | Mass: 10769.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 10771.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 866.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in HIV-1 / Source: (synth.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.8M NaCl 0.1 M MES , pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K | ||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2008 | ||||||||||||||||||||||
Radiation | Monochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||
Reflection | Resolution: 1.8→41.43 Å / Num. all: 19214 / Num. obs: 19176 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 29.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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