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- PDB-7mmj: Crystal structure of HCV NS3/4A D168A protease in complex with NR02-08 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mmj | |||||||||
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Title | Crystal structure of HCV NS3/4A D168A protease in complex with NR02-08 | |||||||||
![]() | NS3 protease | |||||||||
![]() | HYDROLASE/INHIBITOR / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | ![]() transformation of host cell by virus / host cell membrane / serine-type peptidase activity / virion component / symbiont entry into host cell / virion attachment to host cell / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Zephyr, J. / Schiffer, C.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance. Authors: Zephyr, J. / Nageswara Rao, D. / Vo, S.V. / Henes, M. / Kosovrasti, K. / Matthew, A.N. / Hedger, A.K. / Timm, J. / Chan, E.T. / Ali, A. / Kurt Yilmaz, N. / Schiffer, C.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 | ![]() | 108.3 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7mm2C ![]() 7mm3C ![]() 7mm4C ![]() 7mm5C ![]() 7mm6C ![]() 7mm7C ![]() 7mm8C ![]() 7mm9C ![]() 7mmaC ![]() 7mmbC ![]() 7mmcC ![]() 7mmdC ![]() 7mmfC ![]() 7mmgC ![]() 7mmhC ![]() 7mmiC ![]() 7mmkC ![]() 7mmlC ![]() 5vojS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21060.879 Da / Num. of mol.: 1 / Fragment: D168A / Mutation: D168A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 123 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ZJM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZJM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-ZJM / ( | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, pH 6.5, 4% w/v ammonium sulfate, 20-26% PEG3350, cryoprotectant = same + 15% ethylene glycol |
-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: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→25.1 Å / Num. obs: 17598 / % possible obs: 96.69 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.45 Å2 / CC1/2: 0.992 / Net I/σ(I): 7.98 |
Reflection shell | Resolution: 1.992→2.063 Å / Num. unique obs: 1609 / CC1/2: 0.86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5VOJ Resolution: 1.992→25.1 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.899 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 33.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.992→25.1 Å
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Refine LS restraints |
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LS refinement shell |
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