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Yorodumi- PDB-5hlf: STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A 38-MER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hlf | |||||||||
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Title | STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE In COMPLEX WITH A 38-MER HAIRPIN TEMPLATE-PRIMER DNA APTAMER AND AN ALPHA-CARBOXYPHOSPHONATE INHIBITOR | |||||||||
Components |
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Keywords | TRANSFERASE/INHIBITOR/DNA / DNA APTAMER / 2-O-METHYLCYTIDINE / P51 / P66 / TRANSFERASE / NCRTI / Nucleotide competing / Inhibitor / TRANSFERASE-INHIBITOR-DNA complex | |||||||||
Function / homology | Function and homology information HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 group M subtype B synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | |||||||||
Authors | Das, K. / Arnold, E. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Org.Biomol.Chem. / Year: 2016 Title: Exploring the role of the alpha-carboxyphosphonate moiety in the HIV-RT activity of alpha-carboxy nucleoside phosphonates. Authors: Mullins, N.D. / Maguire, N.M. / Ford, A. / Das, K. / Arnold, E. / Balzarini, J. / Maguire, A.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hlf.cif.gz | 453 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hlf.ent.gz | 358.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hlf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hlf_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5hlf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5hlf_validation.xml.gz | 73.8 KB | Display | |
Data in CIF | 5hlf_validation.cif.gz | 98.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hlf ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hlf | HTTPS FTP |
-Related structure data
Related structure data | 5d3gS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-HIV-1 REVERSE TRANSCRIPTASE ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 63875.117 Da / Num. of mol.: 2 / Mutation: D498N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase #2: Protein | Mass: 51928.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase |
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-DNA chain / Sugars , 2 types, 4 molecules EF
#3: DNA chain | Mass: 11748.526 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) #4: Polysaccharide | |
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-Non-polymers , 5 types, 22 molecules
#5: Chemical | #6: Chemical | ChemComp-64A / {[( | #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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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: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 7% PEG 8000, 25 MM BISTRIS-PROPANE PH, 6.8, 75 MM BISTRIS-PROPANE PH 7.4, 50 MM AMMONIUM SULFATE, 5% GLYCEROL, 5% SUCROSE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.95→43.09 Å / Num. obs: 52130 / % possible obs: 84.8 % / Redundancy: 2.1 % / Biso Wilson estimate: 84.87 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.052 / Net I/σ(I): 9.1 / Num. measured all: 110137 / Scaling rejects: 42 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D3G Resolution: 2.95→43 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / 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: 225.79 Å2 / Biso mean: 103.8995 Å2 / Biso min: 29.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→43 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: 18
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