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Yorodumi- PDB-4kko: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kko | ||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-((4-methoxy-6-(2-morpholinoethoxy)-1,3,5-triazin-2-yl)amino)-2-((3-methylbut-2-en-1-yl)oxy)benzonitrile (JLJ513), a non-nucleoside inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Polymerase / Transferase / Hydrolase/inhibitor / Rnase / 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: 2.89 Å | ||||||
Authors | Frey, K.M. / Anderson, K.S. | ||||||
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 | 4kko.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kko.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 4kko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kko_validation.pdf.gz | 686.7 KB | Display | wwPDB validaton report |
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Full document | 4kko_full_validation.pdf.gz | 705.7 KB | Display | |
Data in XML | 4kko_validation.xml.gz | 35 KB | Display | |
Data in CIF | 4kko_validation.cif.gz | 46.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/4kko ftp://data.pdbj.org/pub/pdb/validation_reports/kk/4kko | HTTPS FTP |
-Related structure data
Related structure data | 4ko0C 2zd1S S: Starting model for refinement C: citing same article (ref.) |
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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
#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 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 |
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#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 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-1RE / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17.5% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, and 50 mM citric acid pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2012 / Details: Monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.89→48.845 Å / Num. all: 28695 / Num. obs: 28706 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 81.02 Å2 / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Χ2: 4.02 / Net I/σ(I): 6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code: 2ZD1 Resolution: 2.89→48.845 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7299 / SU ML: 0.44 / σ(F): 1.35 / σ(I): 1.35 / Phase error: 33.19 / Stereochemistry target values: Maximum Likelihood (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: 161.89 Å2 / Biso mean: 58.5786 Å2 / Biso min: 4.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→48.845 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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