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Open data
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Basic information
Entry | Database: PDB / ID: 7led | ||||||
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Title | HIV-1 Protease WT (NL4-3) in Complex with PU4 (LR2-78) | ||||||
![]() | Protease | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HIV / NL4-3 PROTEASE / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() | ||||||
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: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.4 KB | Display | ![]() |
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PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.5 KB | Display | ![]() |
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Full document | ![]() | 787.2 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ldyC ![]() 7ldzC ![]() 7le0C ![]() 7le1C ![]() 7le2C ![]() 7le3C ![]() 7le4C ![]() 7le5C ![]() 7le6C ![]() 7le7C ![]() 7le8C ![]() 7le9C ![]() 7leaC ![]() 7lebC ![]() 7lecC ![]() 7leeC ![]() 7lefC ![]() 7legC ![]() 7lehC ![]() 7leiC ![]() 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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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-XVM / | #4: 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: 2.16 Å3/Da / Density % sol: 42.93 % |
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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: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→24.2 Å / Num. obs: 12221 / % possible obs: 92.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.65 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.996→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 547 / % possible all: 85.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6DGX Resolution: 1.996→24.193 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.37 / 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: 102.32 Å2 / Biso mean: 32.1371 Å2 / Biso min: 13.16 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.996→24.193 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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