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Yorodumi- PDB-6dh3: Crystal structure of HIV-1 Protease NL4-3 V82I Mutant in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dh3 | ||||||
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Title | Crystal structure of HIV-1 Protease NL4-3 V82I Mutant in complex with darunavir | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV / Protease / NL4-3 / 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: 1.908 Å | ||||||
Authors | Lockbaum, G.J. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Infect Dis / Year: 2019 Title: Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. Authors: Lockbaum, G.J. / Leidner, F. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Nachum, G.S. / Nalivaika, E.A. / Ali, A. / Yilmaz, N.K. / 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 | 6dh3.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dh3.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 6dh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/6dh3 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/6dh3 | HTTPS FTP |
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-Related structure data
Related structure data | 6dgxC 6dgyC 6dgzC 6dh0C 6dh1C 6dh2C 6dh4C 6dh5C 6dh6C 6dh7C 6dh8C 4ll3S 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: 10845.859 Da / Num. of mol.: 2 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: Q6B6C5 #2: Chemical | ChemComp-017 / ( | #3: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23-24% (w/v) Ammonium Sulfate, 0.1M Bis-Tris-Methane-HCl Buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: Jun 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.908→24.162 Å / Num. obs: 14540 / % possible obs: 96.9 % / Redundancy: 4.7 % / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.908→2.0549 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LL3 Resolution: 1.908→24.162 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.908→24.162 Å
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Refine LS restraints |
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LS refinement shell |
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