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Yorodumi- PDB-7ahx: HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND D-ASPARTATE TENO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ahx | ||||||
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Title | HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND D-ASPARTATE TENOFOVIR WITH BOUND MANGANESE | ||||||
Components |
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Keywords | TRANSFERASE / reverse transcriptase RT inhibitor complex tenofovir 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 BH10 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Gu, W. / Martinez, S.E. / Nguyen, H. / Xu, H. / Herdewijn, P. / de Jonghe, S. / Das, K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues. Authors: Gu, W. / Martinez, S. / Nguyen, H. / Xu, H. / Herdewijn, P. / De Jonghe, S. / Das, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ahx.cif.gz | 563.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ahx.ent.gz | 364.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ahx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/7ahx ftp://data.pdbj.org/pub/pdb/validation_reports/ah/7ahx | HTTPS FTP |
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-Related structure data
Related structure data | 7aidC 7aifC 7aigC 7aiiC 7aijC 3v4iS 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: 64022.414 Da / Num. of mol.: 2 / Mutation: Q258C, C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds #2: Protein | Mass: 50039.488 Da / Num. of mol.: 2 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 BH10 Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus- ...References: UniProt: P03366, HIV-1 retropepsin, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds |
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-DNA chain , 2 types, 4 molecules TEPF
#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, 114 molecules
#5: Chemical | ChemComp-MN / #6: Chemical | #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: 3.19 Å3/Da / Density % sol: 61.5 % Description: long parallelogram with width greater than thickness |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 16-19.5% v/v PEG Smear Broad, 0.2 M (NH4)2SO4, 0.1 M Tris-HCl PH range: pH 8.3 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→69.8 Å / Num. obs: 84580 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 58.55 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.064 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.73→2.78 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4484 / CC1/2: 0.286 / Rpim(I) all: 0.254 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V4I Resolution: 2.73→69.8 Å / SU ML: 0.4329 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 26.4137 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 77.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→69.8 Å
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Refine LS restraints |
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LS refinement shell |
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