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- PDB-6ogp: X-ray crystal structure of wild type HIV-1 protease in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ogp | ||||||
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Title | X-ray crystal structure of wild type HIV-1 protease in complex with GRL-063 | ||||||
![]() | Protease | ||||||
![]() | VIRAL PROTEIN/INHIBITOR / Inhibitor / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bulut, H. / Hattori, S.I. / Aoki-Ogata, H. / Hayashi, H. / Aoki, M. / Ghosh, A.K. / Mitsuya, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity. Authors: Bulut, H. / Hattori, S.I. / Aoki-Ogata, H. / Hayashi, H. / Das, D. / Aoki, M. / Davis, D.A. / Rao, K.V. / Nyalapatla, P.R. / Ghosh, A.K. / Mitsuya, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.1 KB | Display | ![]() |
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PDB format | ![]() | 24.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380 KB | Display | ![]() |
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Full document | ![]() | 382.8 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 3.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oglC ![]() 6ogqC ![]() 6ogsC ![]() 6ogtC ![]() 6oydC ![]() 6oyrC ![]() 5tyrS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10830.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-MJD / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15 M Ammonium sulfate, 0.1 M HEPES (pH 7.0), 20% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→54.63 Å / Num. obs: 15238 / % possible obs: 100 % / Redundancy: 18.5 % / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 1.53→1.58 Å / Num. unique obs: 15199 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TYR Resolution: 1.53→1.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.4 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.97 Å2
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Refinement step | Cycle: 1 / Resolution: 1.53→1.58 Å
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Refine LS restraints |
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