+Open data
-Basic information
Entry | Database: PDB / ID: 7lee | ||||||
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Title | HIV-1 Protease WT (NL4-3) in Complex with PU5 (LR4-47) | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 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: To Be Published Title: HIV-1 Protease Inhibitors with a P1 Phosphonate Modification Maintain Potency against Drug Resistant Variants by Increased van der Waals Contacts with Flaps Residues 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lee.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lee.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 7lee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lee_validation.pdf.gz | 790.9 KB | Display | wwPDB validaton report |
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Full document | 7lee_full_validation.pdf.gz | 795.5 KB | Display | |
Data in XML | 7lee_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7lee_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/7lee ftp://data.pdbj.org/pub/pdb/validation_reports/le/7lee | HTTPS FTP |
-Related structure data
Related structure data | 7ldyC 7ldzC 7le0C 7le1C 7le2C 7le3C 7le4C 7le5C 7le6C 7le7C 7le8C 7le9C 7leaC 7lebC 7lecC 7ledC 7lefC 7legC 7lehC 7leiC 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 #2: Chemical | ChemComp-XVJ / | #3: Chemical | ChemComp-SO4 / | #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: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23-24% (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: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.795→42.706 Å / Num. obs: 18123 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.795→1.86 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1777 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DGX Resolution: 1.795→42.706 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.92 Å2 / Biso mean: 37.3166 Å2 / Biso min: 15.95 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.795→42.706 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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