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Yorodumi- PDB-4ko0: CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ko0 | ||||||
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Title | CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH an anilinylpyrimidine derivative (JLJ-135) | ||||||
Components | (HIV-1 reverse transcriptase, ...) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / P51/P66 / HETERO DIMER / NNRTI / NONNUCLEOSIDE INHIBITOR / AIDS / HIV / DNA RECOMBINATION / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSFERASE / HYDROLASE-INHIBITOR COMPLEX / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Das, K. / Bauman, J.D. / Arnold, E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Extension into the entrance channel of HIV-1 reverse transcriptase-Crystallography and enhanced solubility. Authors: Bollini, M. / Frey, K.M. / Cisneros, J.A. / Spasov, K.A. / Das, K. / Bauman, J.D. / Arnold, E. / Anderson, K.S. / Jorgensen, W.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ko0.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ko0.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ko0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ko0_validation.pdf.gz | 794.7 KB | Display | wwPDB validaton report |
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Full document | 4ko0_full_validation.pdf.gz | 813.6 KB | Display | |
Data in XML | 4ko0_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 4ko0_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/4ko0 ftp://data.pdbj.org/pub/pdb/validation_reports/ko/4ko0 | HTTPS FTP |
-Related structure data
Related structure data | 4kkoC 1s9eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: p66 / Mutation: K172A, K173A, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: 1B1 / Gene: gag-pol / Plasmid: PRT52A / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 / References: UniProt: P03366, RNA-directed DNA polymerase |
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#2: Protein | Mass: 50039.488 Da / Num. of mol.: 1 / Fragment: p51 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: 1B1 / Gene: gag-pol / Plasmid: PRT52A / Production host: Escherichia coli (E. coli) / Strain (production host): BH10 / References: UniProt: P03366, RNA-directed DNA polymerase |
-Non-polymers , 4 types, 343 molecules
#3: Chemical | ChemComp-JLJ / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 277 K / pH: 6.8 Details: PEG 8000, AMMONIUM SULFATE, MGCL2, IMIDAZOLE , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2006 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 91737 / % possible obs: 98.8 % / Observed criterion σ(I): -1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S9E Resolution: 1.95→29.31 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 29.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.01 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→29.31 Å
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Refine LS restraints |
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LS refinement shell |
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