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Yorodumi- PDB-6dv0: HIV-1 wild type protease with GRL-02815A, a thiochroman heterocyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dv0 | ||||||||||||||||||
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Title | HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine functionality as the P2 ligand | ||||||||||||||||||
Components | Protease | ||||||||||||||||||
Keywords | HYDROLASE / ANTIVIRAL PROTEIN / aspartic acid protease / HIV-1 protease inhibitor of GRL-02815A / thiochroman / P2 ligand / drug resistance / design and synthesis | ||||||||||||||||||
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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / 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 / Early Phase of HIV Life Cycle / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / Assembly Of The HIV Virion / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / Budding and maturation of HIV virion / host multivesicular body / protein processing / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / peptidase activity / 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 / viral translational frameshifting / 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: 1.2 Å | ||||||||||||||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | ||||||||||||||||||
Funding support | United States, Japan, 5items
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Citation | Journal: Eur J Med Chem / Year: 2018 Title: Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. Authors: Ghosh, A.K. / Jadhav, R.D. / Simpson, H. / Kovela, S. / Osswald, H. / Agniswamy, J. / Wang, Y.F. / Hattori, S.I. / Weber, I.T. / Mitsuya, H. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dv0.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dv0.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dv0_validation.pdf.gz | 1018.9 KB | Display | wwPDB validaton report |
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Full document | 6dv0_full_validation.pdf.gz | 1022.8 KB | Display | |
Data in XML | 6dv0_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6dv0_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/6dv0 ftp://data.pdbj.org/pub/pdb/validation_reports/dv/6dv0 | HTTPS FTP |
-Related structure data
Related structure data | 6dv4C 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RZ08, UniProt: P04585*PLUS |
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-Non-polymers , 5 types, 211 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-GA8 / | #6: 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: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.90M NaCl, 0.1M Sodium Cacodylate pH 6.4 / PH range: 6.4 |
-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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 67382 / % possible obs: 91.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 3797 / % possible all: 52.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NU3 Resolution: 1.2→50 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: 55 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1734.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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