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Yorodumi- PDB-7otk: HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND INHIBITOR RMC-233 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7otk | ||||||
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Title | HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND INHIBITOR RMC-233 | ||||||
Components |
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Keywords | TRANSFERASE / REVERSE TRANSCRIPTASE / RT INHIBITOR COMPLEX / ACYCLIC NUCLEOSIDE PHOSPHONATE ANALOG / RT-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 / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 group M subtype B Human immunodeficiency virus type 1 BH10 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Martinez, S.E. / Singh, A.K. / Gu, W. / Das, K. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2021 Title: Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design. Authors: Gu, W. / Martinez, S. / Singh, A.K. / Nguyen, H. / Rozenski, J. / Schols, D. / Herdewijn, P. / Das, K. / De Jonghe, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7otk.cif.gz | 457.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7otk.ent.gz | 362.3 KB | Display | PDB format |
PDBx/mmJSON format | 7otk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7otk_validation.pdf.gz | 789.6 KB | Display | wwPDB validaton report |
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Full document | 7otk_full_validation.pdf.gz | 838.4 KB | Display | |
Data in XML | 7otk_validation.xml.gz | 70.1 KB | Display | |
Data in CIF | 7otk_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7otk ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7otk | HTTPS FTP |
-Related structure data
Related structure data | 7ot6C 7otaC 7otnC 7otxC 7otzC 7outC 3v4iS C: citing same article (ref.) S: Starting model for refinement |
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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
-Reverse transcriptase/ribonuclease ... , 2 types, 4 molecules CADB
#1: Protein | Mass: 64022.414 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 BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H #2: Protein | Mass: 50039.488 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 BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H |
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-DNA chain , 2 types, 4 molecules ETFP
#3: DNA chain | Mass: 8383.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus type 1 BH10 #4: DNA chain | Mass: 6474.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 3 types, 5 molecules
#5: Chemical | ChemComp-MG / |
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#6: Chemical | ChemComp-1IA / ( |
#7: 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: 3.17 Å3/Da / Density % sol: 61.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 16-19% V/V PEG SMEAR BROAD, 0.2 M (NH4)2SO4, 0.1 M TRIS-HCL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→61.88 Å / Num. obs: 67827 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 96.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.95→3.02 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.8 / Num. unique obs: 4588 / CC1/2: 0.281 / Rpim(I) all: 0.737 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V4I Resolution: 2.95→61.11 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.43 / 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: 380.52 Å2 / Biso mean: 118.6106 Å2 / Biso min: 24.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→61.11 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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