[English] 日本語
Yorodumi- PDB-4o4g: Crystal Structure of HIV-1 Reverse Transcriptase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o4g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of HIV-1 Reverse Transcriptase in complex with 4-((4-(mesitylamino)-1,3,5-triazin-2-yl)amino)benzonitrile (JLJ527), a non-nucleoside inhibitor | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Polymerase / RNase / reverse transcription / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 | Human immunodeficiency virus type 1 BH10 Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.712 Å | ||||||
Authors | Mislak, A.C. / Frey, K.M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: A mechanistic and structural investigation of modified derivatives of the diaryltriazine class of NNRTIs targeting HIV-1 reverse transcriptase. Authors: Mislak, A.C. / Frey, K.M. / Bollini, M. / Jorgensen, W.L. / Anderson, K.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4o4g.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4o4g.ent.gz | 168.1 KB | Display | PDB format |
PDBx/mmJSON format | 4o4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o4g_validation.pdf.gz | 751.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4o4g_full_validation.pdf.gz | 775.7 KB | Display | |
Data in XML | 4o4g_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 4o4g_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/4o4g ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o4g | HTTPS FTP |
-Related structure data
Related structure data | 4o44C 2zd1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: p66 subunit, UNP residues 600-1154 / Mutation: C280S, K172A, K173A Source method: isolated from a genetically manipulated source Details: Lentivirus Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Strain: Bh10 Isolate / Gene: gag-pol / Plasmid: pCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366, RNA-directed DNA polymerase |
---|---|
#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 subunit, UNP residues 600-1027 / Mutation: C280S Source method: isolated from a genetically manipulated source Details: Lentivirus / Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: Bh10 Isolate / Gene: gag-pol / Plasmid: pCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-2RT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20.0% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine-HCl, and 50 mM citric acid pH 5.5 or 50 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2013 / Details: Monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.63→50 Å / Num. obs: 38084 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 70.95 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.065 / Net I/σ(I): 29.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZD1 Resolution: 2.712→43.239 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 32.36 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.712→43.239 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|