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- PDB-5fdl: Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcripta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fdl | ||||||
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Title | Crystal Structure of K103N/Y181C Mutant HIV-1 Reverse Transcriptase (RT) in Complex with IDX899 | ||||||
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![]() | HYDROLASE / HIV-1 Reverse Transcriptase / Phosphoindole / NNRTI / Mutation | ||||||
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 / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dousson, C.B. / Alexandre, F.-R. / Convard, T. / Fisher, M. / Lamers, M.B.A.C. / Leonard, P.M. | ||||||
![]() | ![]() Title: Discovery of the Aryl-phospho-indole IDX899, a Highly Potent Anti-HIV Non-nucleoside Reverse Transcriptase Inhibitor. Authors: Dousson, C. / Alexandre, F.R. / Amador, A. / Bonaric, S. / Bot, S. / Caillet, C. / Convard, T. / da Costa, D. / Lioure, M.P. / Roland, A. / Rosinovsky, E. / Maldonado, S. / Parsy, C. / ...Authors: Dousson, C. / Alexandre, F.R. / Amador, A. / Bonaric, S. / Bot, S. / Caillet, C. / Convard, T. / da Costa, D. / Lioure, M.P. / Roland, A. / Rosinovsky, E. / Maldonado, S. / Parsy, C. / Trochet, C. / Storer, R. / Stewart, A. / Wang, J. / Mayes, B.A. / Musiu, C. / Poddesu, B. / Vargiu, L. / Liuzzi, M. / Moussa, A. / Jakubik, J. / Hubbard, L. / Seifer, M. / Standring, 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 | ![]() | 196.8 KB | Display | ![]() |
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PDB format | ![]() | 155.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743.1 KB | Display | ![]() |
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Full document | ![]() | 745 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 43.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ko0S S: Starting model for refinement |
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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: 64086.426 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: P51 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 51295.926 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: P66 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-5DV / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein was concentrated to 14 mg/ml in the presence of 0.5 mM inhibitor A051606P then used in successive crystal micro-seeding experiments to yield protein crystals of 0.3 mm x 0.3 mm x 0.2 ...Details: Protein was concentrated to 14 mg/ml in the presence of 0.5 mM inhibitor A051606P then used in successive crystal micro-seeding experiments to yield protein crystals of 0.3 mm x 0.3 mm x 0.2 mm in 1.4 M Sodium Malonate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→94.15 Å / Num. obs: 26048 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KO0 Resolution: 3.1→94.15 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.845 / SU B: 30.378 / SU ML: 0.495 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.782 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→94.15 Å
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