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Yorodumi- PDB-6dj2: HIV-1 protease with single mutation L76V in complex with Lopinavir -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dj2 | ||||||
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Title | HIV-1 protease with single mutation L76V in complex with Lopinavir | ||||||
Components | HIV-1 protease | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Antiviral agents / protein-inhibitor structures / HIV drug resistance / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / Budding and maturation of HIV virion / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase activity / 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 / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Wang, Y.-F. / Wong-Sam, A.E. / Zhang, Y. / Weber, I.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Omega / Year: 2018 Title: Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease. Authors: Wong-Sam, A. / Wang, Y.F. / Zhang, Y. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dj2.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dj2.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dj2_validation.pdf.gz | 780.5 KB | Display | wwPDB validaton report |
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Full document | 6dj2_full_validation.pdf.gz | 781.3 KB | Display | |
Data in XML | 6dj2_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6dj2_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/6dj2 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/6dj2 | HTTPS FTP |
-Related structure data
Related structure data | 6difC 6dilC 6dj1C 6dj5C 6dj7C 3nu3S 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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Unit cell |
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-Components
#1: Protein | Mass: 10726.650 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, L76V, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5RZ08, UniProt: P04585*PLUS #2: Chemical | ChemComp-NA / | #3: Chemical | #4: Chemical | ChemComp-AB1 / | #5: 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: 2.77 Å3/Da / Density % sol: 55.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.9 M NaCl, 5% DMSO, 0.1 M citrate phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 47855 / % possible obs: 91.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.36→1.41 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2767 / % possible all: 53.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.36→28 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 45 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1780.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.41 Å /
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