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Yorodumi- PDB-6x4b: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x4b | |||||||||
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Title | Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-5-fluoro-8-methyl-2-naphthonitrile (JLJ655), a Non-nucleoside Inhibitor | |||||||||
Components |
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Keywords | TRANSFERASE / HYDROLASE/INHIBITOR / Polymerase / reverse transcriptase / non-nucleoside inhibitor / 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 group M subtype B | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Chan, A.H. / Duong, V.N. / Ippolito, J.A. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site. Authors: Duong, V.N. / Ippolito, J.A. / Chan, A.H. / Lee, W.G. / Spasov, K.A. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x4b.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x4b.ent.gz | 162.5 KB | Display | PDB format |
PDBx/mmJSON format | 6x4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x4b_validation.pdf.gz | 796.4 KB | Display | wwPDB validaton report |
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Full document | 6x4b_full_validation.pdf.gz | 807 KB | Display | |
Data in XML | 6x4b_validation.xml.gz | 34 KB | Display | |
Data in CIF | 6x4b_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/6x4b ftp://data.pdbj.org/pub/pdb/validation_reports/x4/6x4b | HTTPS FTP |
-Related structure data
Related structure data | 6x47C 6x49C 6x4aC 6x4cC 6x4dC 6x4eC 6x4fC 5terS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: C280S, K172A, K173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
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#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 group M subtype B Gene: gag-pol / Plasmid: PCDF-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03366 |
-Non-polymers , 4 types, 50 molecules
#3: Chemical | ChemComp-UMY / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.61 % / Mosaicity: 0.214 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 mM imidazole pH 6.5, 18% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 50178 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Χ2: 2.782 / Net I/σ(I): 10.9 / Num. measured all: 189646 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TER Resolution: 2.5→41.423 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.15 / Stereochemistry target values: 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: 130.08 Å2 / Biso mean: 56.0119 Å2 / Biso min: 23.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→41.423 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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