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- PDB-5tuq: Crystal Structure of a 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tuq | ||||||
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Title | Crystal Structure of a 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione Inhibitor in Complex with HIV Reverse Transcriptase | ||||||
![]() | (HIV-1 REVERSE TRANSCRIPTASE) x 2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / HIV-1 / REVERSE TRANSCRIPTASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kirby, K.A. / Sarafianos, S.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase. Authors: Tang, J. / Kirby, K.A. / Huber, A.D. / Casey, M.C. / Ji, J. / Wilson, D.J. / Sarafianos, S.G. / Wang, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 418.4 KB | Display | ![]() |
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PDB format | ![]() | 343.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4g1qS 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: 64105.441 Da / Num. of mol.: 1 / Fragment: p66 domain residues 600-1154 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET35a / Production host: ![]() ![]() References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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#2: Protein | Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: p51 domain residues 600-1027 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET35a / Production host: ![]() ![]() References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
#3: Chemical | ChemComp-J63 / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.64 % / Mosaicity: 0.18 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.1 Details: PEG 3350, SODIUM POTASSIUM PHOSPHATE, ETHYLENE GLYCOL, MES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→48.02 Å / Num. obs: 33593 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 77.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.033 / Rrim(I) all: 0.092 / Net I/σ(I): 14.7 / Num. measured all: 254208 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G1Q Resolution: 2.705→48.022 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 182.46 Å2 / Biso mean: 97.21 Å2 / Biso min: 46.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.705→48.022 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 41.2839 Å / Origin y: -0.9885 Å / Origin z: 28.5384 Å
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Refinement TLS group |
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