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- PDB-5c25: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5c25 | ||||||||||||||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 6-((4-((4-cyanophenyl)amino)-1,3,5-triazin-2-yl)amino)-5,7-dimethyl-2-naphthonitrile (JLJ639), a Non-nucleoside Inhibitor | ||||||||||||||||||
![]() | (HIV-1 REVERSE TRANSCRIPTASE, ...) x 2 | ||||||||||||||||||
![]() | TRANSFERASE / HYDROLASE/INHIBITOR / Polymerase / reverse transcriptase / HIV / non-nucleoside inhibitor / HYDROLASE-DNA-INHIBITOR complex / HYDROLASE-INHIBITOR complex | ||||||||||||||||||
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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Chan, A.H. / Frey, K.M. / Anderson, K.S. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase. Authors: Lee, W.G. / Frey, K.M. / Gallardo-Macias, R. / Spasov, K.A. / Chan, A.H. / Anderson, K.S. / Jorgensen, W.L. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210 KB | Display | ![]() |
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PDB format | ![]() | 165 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.2 KB | Display | ![]() |
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Full document | ![]() | 767.3 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c24C ![]() 2zd1S C: citing same article ( 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
-HIV-1 REVERSE TRANSCRIPTASE, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: UNP residues 600-1154 / Mutation: C280S, K172A, K173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / 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: 50039.488 Da / Num. of mol.: 1 / Fragment: UNP residues 600-1027 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate BH10 / Gene: gag-pol / Plasmid: PCDF-2 / Production host: ![]() ![]() References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
-Non-polymers , 4 types, 31 molecules ![](data/chem/img/639.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-639 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 14% PEG 8000, 100 mM Ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, 15 mM HEPES pH 7.0 PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→50 Å / Num. obs: 29671 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 49.07 Å2 / Rsym value: 0.146 / Net I/σ(I): 14.61 |
Reflection shell | Resolution: 2.84→3.01 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.95 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZD1 Resolution: 2.841→43.458 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.74 / Phase error: 29.1 / 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 mean: 47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.841→43.458 Å
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Refine LS restraints |
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LS refinement shell |
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