[English] 日本語
Yorodumi- PDB-3qo9: Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qo9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of HIV-1 Reverse Transcriptase (RT) in complex with TSAO-T, a non-nucleoside RT inhibitor (NNRTI) | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / HYDROLASE/INHIBITOR / AIDS / HIV / RNA-BINDING / RNA-DIRECTED DNA POLYMERASE / VIRAL NUCLEOPROTEIN / nonnucleoside / NNRTI / 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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Das, K. / Arnold, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Crystal Structure of tert-Butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in Complex with HIV-1 Reverse Transcriptase (RT) Redefines the Elastic Limits of the Non-nucleoside ...Title: Crystal Structure of tert-Butyldimethylsilyl-spiroaminooxathioledioxide-thymine (TSAO-T) in Complex with HIV-1 Reverse Transcriptase (RT) Redefines the Elastic Limits of the Non-nucleoside Inhibitor-Binding Pocket. Authors: Das, K. / Bauman, J.D. / Rim, A.S. / Dharia, C. / Clark, A.D. / Camarasa, M.J. / Balzarini, J. / Arnold, E. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations #2: Journal: J.Med.Chem. / Year: 2004 Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent ...Title: Roles of Conformational and Positional Adaptability in Structure-Based Design of Tmc125-R165335 (Etravirine) and Related Non-Nucleoside Reverse Transcriptase Inhibitors that are Highly Potent and Effective Against Wild-Type and Drug-Resistant HIV-1 Variants. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qo9.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qo9.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qo9_validation.pdf.gz | 886.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3qo9_full_validation.pdf.gz | 935.4 KB | Display | |
Data in XML | 3qo9_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 3qo9_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qo9 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qo9 | HTTPS FTP |
-Related structure data
Related structure data | 2zd1S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 64045.348 Da / Num. of mol.: 1 / Mutation: F160S, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Strain: BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
---|---|
#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, DNA-directed DNA polymerase, ribonuclease H |
#3: Chemical | ChemComp-QO9 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.89 % |
---|---|
Crystal grow | Temperature: 279 K / Method: evaporation / pH: 6.8 Details: PEG8000, 50mM imidazole pH 6.8 and 0.1M ammonium sulfate, EVAPORATION, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 23, 2009 |
Radiation | Monochromator: VariMax-HR optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 37564 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / Num. unique all: 1855 / % possible all: 97.8 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZD1 Resolution: 2.6→48.27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.27 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.63 Å
|