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Yorodumi- PDB-5k14: HIV-1 Reverse Transcriptase in complex with a 2,6-difluorophenyl ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k14 | ||||||
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Title | HIV-1 Reverse Transcriptase in complex with a 2,6-difluorophenyl DAPY analog | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / HIV-1 / reverse transcriptase / NNRTI / inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / symbiont-mediated activation of host apoptosis / HIV-1 retropepsin / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / 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 / peptidase activity / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.402 Å | ||||||
Authors | Lansdon, E.B. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Novel (2,6-difluorophenyl)(2-(phenylamino)pyrimidin-4-yl)methanones with restricted conformation as potent non-nucleoside reverse transcriptase inhibitors against HIV-1. Authors: Simon, P. / Baszczynski, O. / Saman, D. / Stepan, G. / Hu, E. / Lansdon, E.B. / Jansa, P. / Janeba, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k14.cif.gz | 205.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k14.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 5k14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k14_validation.pdf.gz | 766.7 KB | Display | wwPDB validaton report |
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Full document | 5k14_full_validation.pdf.gz | 794.4 KB | Display | |
Data in XML | 5k14_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 5k14_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/5k14 ftp://data.pdbj.org/pub/pdb/validation_reports/k1/5k14 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64562.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) Strain: isolate HXB2 / Gene: gag-pol / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P04585 |
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#2: Protein | Mass: 51399.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate LW123) Strain: isolate LW123 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6F2, RNA-directed DNA polymerase |
#3: Chemical | ChemComp-IB1 / |
#4: 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: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.0M K/Na tartrate 100mM MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 58564 / % possible obs: 96.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 98.2 |
-Processing
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Refinement | Resolution: 2.402→47.268 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→47.268 Å
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Refine LS restraints |
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LS refinement shell |
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