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Open data
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Basic information
Entry | Database: PDB / ID: 6pjg | ||||||
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Title | HIV-1 Protease NL4-3 WT in Complex with LR3-97 | ||||||
![]() | Protease NL4-3 | ||||||
![]() | hydrolase/hydrolase inhibitor / HIV / NL4-3 PROTEASE / DRUG RESISTANCE / PROTEASE INHIBITOR / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() : / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...: / : / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 66.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 717.9 KB | Display | ![]() |
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Full document | ![]() | 720.3 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pjbC ![]() 6pjcC ![]() 6pjdC ![]() 6pjeC ![]() 6pjfC ![]() 6pjhC ![]() 6pjiC ![]() 6pjkC ![]() 6pjlC ![]() 6pjmC ![]() 6pjnC ![]() 6pjoC ![]() 6dgxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10831.833 Da / Num. of mol.: 2 / Mutation: Q7K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ORV / ( | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop 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: ![]() ![]() ![]() |
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: 1.8→50 Å / Num. obs: 17695 / % possible obs: 98.7 % / Redundancy: 5.1 % / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.8→1.9101 Å / Num. unique obs: 2788 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6DGX Resolution: 1.8→42.581 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.581 Å
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Refine LS restraints |
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LS refinement shell |
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