+Open data
-Basic information
Entry | Database: PDB / ID: 6pji | ||||||
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Title | HIV-1 Protease NL4-3 WT in Complex with LR3-43 | ||||||
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 HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / 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 / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lockbaum, G.J. / Rusere, L.N. / Henes, M. / Kosovrasti, K. / Lee, S.K. / Spielvogel, E. / Nalivaika, E.A. / Swanstrom, R. / KurtYilmaz, N. / Schiffer, C.A. / Ali, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere. Authors: Rusere, L.N. / Lockbaum, G.J. / Henes, M. / Lee, S.K. / Spielvogel, E. / Rao, D.N. / Kosovrasti, K. / Nalivaika, E.A. / Swanstrom, R. / Kurt Yilmaz, N. / Schiffer, C.A. / Ali, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pji.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pji.ent.gz | 65.6 KB | Display | PDB format |
PDBx/mmJSON format | 6pji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pji_validation.pdf.gz | 786.7 KB | Display | wwPDB validaton report |
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Full document | 6pji_full_validation.pdf.gz | 791.2 KB | Display | |
Data in XML | 6pji_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6pji_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/6pji ftp://data.pdbj.org/pub/pdb/validation_reports/pj/6pji | HTTPS FTP |
-Related structure data
Related structure data | 6pjbC 6pjcC 6pjdC 6pjeC 6pjfC 6pjgC 6pjhC 6pjkC 6pjlC 6pjmC 6pjnC 6pjoC 6dgxS 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: 10831.833 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: Q8ULI9, UniProt: P12497*PLUS #2: Chemical | ChemComp-OO4 / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.14 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 23-27% (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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07812 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 15198 / % possible obs: 99 % / Redundancy: 5.9 % / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.9→2.0382 Å / Num. unique obs: 2903 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DGX Resolution: 1.9→39.373 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.373 Å
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Refine LS restraints |
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LS refinement shell |
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