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- PDB-6pu8: Room temperature X-ray structure of HIV-1 protease triple mutant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pu8 | ||||||
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Title | Room temperature X-ray structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate of keto-darunavir | ||||||
![]() | HIV-1 protease | ||||||
![]() | HYDROLASE / HIV-1 protease / aspartic protease / tetrahedral intermediate inhibitor / homodimer | ||||||
Function / homology | ![]() aspartic-type endopeptidase activity / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kovalevsky, A. / Das, A. | ||||||
![]() | ![]() Title: Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. Authors: Kumar, M. / Mandal, K. / Blakeley, M.P. / Wymore, T. / Kent, S.B.H. / Louis, J.M. / Das, A. / Kovalevsky, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.9 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kmpC ![]() 6ptpC ![]() 5e5jS 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
#1: Protein | Mass: 10754.703 Da / Num. of mol.: 2 / Mutation: V32I,I47V,V82I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-P3V / ( | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 1.0 M NaCl, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 22743 / % possible obs: 98 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2253 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E5J Resolution: 1.8→20 Å / Num. parameters: 6699 / Num. restraintsaints: 6296 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1658.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→20 Å
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Refine LS restraints |
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