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- PDB-2ykm: Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ykm | ||||||
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Title | Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex with a Difluoromethylbenzoxazole (DFMB) Pyrimidine Thioether derivative, a non-nucleoside RT inhibitor (NNRTI) | ||||||
![]() | (REVERSE TRANSCRIPTASE/RIBONUCLEASE H) x 2 | ||||||
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Function / homology | ![]() : / : / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boyer, J. / Arnoult, E. / Medebielle, M. / Guillemont, J. / Unge, T. / Unge, J. / Jochmans, D. | ||||||
![]() | ![]() Title: Difluoromethylbenzoxazole Pyrimidine Thioether Derivatives: A Novel Class of Potent Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors. Authors: Boyer, J. / Arnoult, E. / Medebielle, M. / Guillemont, J. / Unge, J. / Jochmans, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214 KB | Display | ![]() |
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PDB format | ![]() | 171.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 64780.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 600-1156 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: P03366, ![]() ![]() ![]() |
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#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: RESIDUES 600-1027 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: P03366, ![]() ![]() ![]() |
#3: Chemical | ChemComp-YKN / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / ![]() |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 11, 2008 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→20.75 Å / Num. obs: 36314 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: REVERSE TRANSCRIPTASE Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.854 / SU B: 17.96 / SU ML: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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