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Yorodumi- PDB-6opw: HIV-1 Protease NL4-3 I13V, G16E, V32I, L33F, K45I, M46I, A71V, V8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6opw | ||||||
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Title | HIV-1 Protease NL4-3 I13V, G16E, V32I, L33F, K45I, M46I, A71V, V82F, I84V Mutant in complex with darunavir | ||||||
Components | Protease NL4-3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lockbaum, G.J. / Henes, M. / Kosovrasti, K. / Leidner, F. / Nachum, G.S. / Nalivaika, E.A. / Bolon, D.N.A. / KurtYilmaz, N. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. Authors: Henes, M. / Lockbaum, G.J. / Kosovrasti, K. / Leidner, F. / Nachum, G.S. / Nalivaika, E.A. / Lee, S.K. / Spielvogel, E. / Zhou, S. / Swanstrom, R. / Bolon, D.N.A. / Kurt Yilmaz, N. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6opw.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6opw.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 6opw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6opw_validation.pdf.gz | 793.1 KB | Display | wwPDB validaton report |
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Full document | 6opw_full_validation.pdf.gz | 796.9 KB | Display | |
Data in XML | 6opw_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6opw_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6opw ftp://data.pdbj.org/pub/pdb/validation_reports/op/6opw | HTTPS FTP |
-Related structure data
Related structure data | 6opsC 6optC 6opuC 6opvC 6opxC 6opyC 6opzC 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
#1: Protein | Mass: 10965.921 Da / Num. of mol.: 2 Mutation: I13V, G16E, V32I, L33F, K45I, M46I, A71V, V82F, I84V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZCI0, UniProt: P12497*PLUS #2: Chemical | ChemComp-SO4 / | #3: Chemical | ChemComp-017 / ( | #4: 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: 2.09 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 19-26% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 10571 / % possible obs: 99.9 % / Redundancy: 10.5 % / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 2.102→2.3138 Å / Num. unique obs: 2614 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→24.778 Å / Cross valid method: FREE R-VALUE / σ(F): 5.25 / Phase error: 36.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.778 Å
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Refine LS restraints |
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LS refinement shell |
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