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Yorodumi- PDB-6kdn: HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP terna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kdn | ||||||
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Title | HIV-1 reverse transcriptase with Q151M/Y115F/F116Y:DNA:dGTP ternary complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Entecavir 5'-triphosphate / HIV-1 / HBV / reverse transcriptase / drug resistance / drug sensitivity / TRANSFERASE-DNA complex / REPLICATION | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 Human immunodeficiency virus type 1 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å | ||||||
Authors | Yasutake, Y. / Hattori, S.I. / Tamura, N. / Maeda, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: Structural features in common of HBV and HIV-1 resistance against chirally-distinct nucleoside analogues entecavir and lamivudine. Authors: Yasutake, Y. / Hattori, S.I. / Tamura, N. / Matsuda, K. / Kohgo, S. / Maeda, K. / Mitsuya, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kdn.cif.gz | 892.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kdn.ent.gz | 731.1 KB | Display | PDB format |
PDBx/mmJSON format | 6kdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kdn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6kdn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6kdn_validation.xml.gz | 73.3 KB | Display | |
Data in CIF | 6kdn_validation.cif.gz | 100 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdn ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdn | HTTPS FTP |
-Related structure data
Related structure data | 6kdjC 6kdkC 6kdmC 6kdoC 5xn1S 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 64033.387 Da / Num. of mol.: 2 / Mutation: Y214F, F215Y, Q250M, C261S, C379S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pCDF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: D3XFN5, UniProt: P12497*PLUS #2: Protein | Mass: 51861.547 Da / Num. of mol.: 2 / Mutation: C749S, C867S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P12497 |
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-DNA chain , 1 types, 2 molecules EF
#3: DNA chain | Mass: 11724.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 451 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: BIS-TRIS-HCL, DI-AMMONIUM HYDROGEN CITRATE, MGCL2, PEG 6000, SUCROSE, GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 130151 / % possible obs: 100 % / Redundancy: 5.2 % / Rrim(I) all: 0.069 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6400 / Rrim(I) all: 0.888 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XN1 Resolution: 2.303→48.603 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→48.603 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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