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Yorodumi- PDB-6opx: HIV-1 Protease NL4-3 I13V, G16E, V32I, L33F, K45I, M46I, L76V, V8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6opx | ||||||
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Title | HIV-1 Protease NL4-3 I13V, G16E, V32I, L33F, K45I, M46I, L76V, 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 | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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 | 6opx.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6opx.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 6opx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6opx ftp://data.pdbj.org/pub/pdb/validation_reports/op/6opx | HTTPS FTP |
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-Related structure data
Related structure data | 6opsC 6optC 6opuC 6opvC 6opwC 6opyC 6opzC 6dh0S 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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Unit cell |
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-Components
#1: Protein | Mass: 10923.841 Da / Num. of mol.: 2 Mutation: Q7QK, I13V, G16E, V32I, L33F, K45I, M46I, L76V, 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 #2: Chemical | ChemComp-017 / ( | #3: 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: 2.06 Å3/Da / Density % sol: 40.36 % |
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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 3, 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: 2.03→50 Å / Num. obs: 11470 / % possible obs: 99.5 % / Redundancy: 11.1 % / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 2.032→2.2359 Å / Num. unique obs: 2817 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DH0 Resolution: 2.03→22.39 Å / Cross valid method: FREE R-VALUE / σ(F): 7.3 / Phase error: 31.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→22.39 Å
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Refine LS restraints |
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LS refinement shell |
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