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- PDB-6o5a: Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6o5a | ||||||
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Title | Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 with a substrate analog p2-NC in P61 | ||||||
![]() | HIV-1 protease | ||||||
![]() | HYDROLASE / Viral Protein / HIV PROTEASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues. Authors: Agniswamy, J. / Kneller, D.W. / Brothers, R. / Wang, Y.F. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 78.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 927.9 KB | Display | ![]() |
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Full document | ![]() | 939.6 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o48C ![]() 6o54C ![]() 6o57C ![]() 6o5xC ![]() 1sguS C: citing same article ( S: Starting model for refinement |
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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: 10791.594 Da / Num. of mol.: 2 / Mutation: M46L, G48V, C67A, V77I, A82S, I93L, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-2NC / | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 35% TacsimateTM, pH 7.0 (Hampton Research Corp., Aliso Viejo, CA). Tacsimate contains 1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M ...Details: 35% TacsimateTM, pH 7.0 (Hampton Research Corp., Aliso Viejo, CA). Tacsimate contains 1.83 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium tartrate dibasic. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. obs: 21945 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Χ2: 1 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2 / Num. unique obs: 1989 / CC1/2: 0.641 / Rpim(I) all: 0.34 / Χ2: 1.004 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SGU Resolution: 1.67→33.22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.245 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.109 Details: initially refined by SHELX-2014 but moved to REFMAC during later cycles of refinement.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.165 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→33.22 Å
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Refine LS restraints |
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