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Yorodumi- PDB-6dj7: HIV-1 protease with mutation L76V in complex with GRL-5010 (gem-d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dj7 | ||||||
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Title | HIV-1 protease with mutation L76V in complex with GRL-5010 (gem-difluoro-bis-tetrahydrofuran as P2 ligand) | ||||||
Components | HIV-1 protease | ||||||
Keywords | HYDROLASE / Antiviral agents / HIV drug resistance / ANTIVIRAL PROTEIN | ||||||
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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / Uncoating of the HIV Virion / 2-LTR circle formation / 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 / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / 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 / peptidase 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 / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Wong-Sam, A.E. / Wang, Y.F. / 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 | 6dj7.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dj7.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 6dj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/6dj7 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/6dj7 | HTTPS FTP |
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-Related structure data
Related structure data | 6difC 6dilC 6dj1C 6dj2C 6dj5C 3nu3S 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 6 types, 198 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-G10 / ( | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 1.15 M NaCl, 0.1 M NaOAc, pH 5.2 4.1 mg/ml protease stock, 1:5 protease to inhibitor 1:1 liquor to sample, soaked in 30% glycerol cryoprotectant PH range: 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 28, 2016 |
Radiation | Monochromator: Y / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→50 Å / Num. obs: 55212 / % possible obs: 96 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.31→1.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.1 / % possible all: 77.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.31→32 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: 99 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1703.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→32 Å
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Refine LS restraints |
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