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- PDB-4m8x: GS-8374, a Novel Phosphonate-Containing Inhibitor of HIV-1 Protea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m8x | ||||||
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Title | GS-8374, a Novel Phosphonate-Containing Inhibitor of HIV-1 Protease, Effectively Inhibits HIV PR Mutants with Amino Acid Insertions | ||||||
![]() | Protease | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / HIV protease / aspartic protease / GS8374 / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grantz saskova, K. / Brynda, J. / Rezacova, P. / Kozisek, M. / Konvalinka, J. | ||||||
![]() | ![]() Title: GS-8374, a prototype phosphonate-containing inhibitor of HIV-1 protease, effectively inhibits protease mutants with amino acid insertions. Authors: Grantz Saskova, K. / Kozisek, M. / Stray, K. / de Jong, D. / Rezaova, P. / Brynda, J. / van Maarseveen, N.M. / Nijhuis, M. / Cihlar, T. / Konvalinka, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.1 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1022.3 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m8yC ![]() 2rkfS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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Components
#1: Protein | Mass: 10783.658 Da / Num. of mol.: 2 / Mutation: L10F, I13V, G16A, K20M, D37S, I46V, I54M, A71V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop Details: 0.5 M ammonium sulphate and 0.1 M sodium acetate pH 5.25-5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K PH range: 5.25-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.05 Å / Num. all: 11333 / Num. obs: 10764 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2RKF Resolution: 2.05→53.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 16.431 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.222 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.426 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→53.45 Å
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Refine LS restraints |
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