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- PDB-7mmd: Crystal structure of HCV NS3/4A D168A protease in complex with JZ01-19 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mmd | |||||||||
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Title | Crystal structure of HCV NS3/4A D168A protease in complex with JZ01-19 | |||||||||
![]() | NS3/4A protease | |||||||||
![]() | HYDROLASE/INHIBITOR / NS3/4a Protease / Hepatitis C virus / Drug Resistance / Protease inhibitor / HYDROLASE-INHIBITOR complex / VIRAL PROTEIN | |||||||||
Function / homology | ![]() host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization ...host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm 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 | ![]() | 66.1 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 ![]() 7mmfC ![]() 7mmgC ![]() 7mmhC ![]() 7mmiC ![]() 7mmjC ![]() 7mmkC ![]() 7mmlC ![]() 5vojS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 21218.074 Da / Num. of mol.: 1 / Mutation: D168A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 178 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZJP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZJP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-ZJP / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350 The cryogenic condition is 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350, 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: Jul 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→23.78 Å / Num. obs: 13836 / % possible obs: 85.88 % / Redundancy: 4 % / Biso Wilson estimate: 12.68 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.13 |
Reflection shell | Resolution: 1.89→1.958 Å / Num. unique obs: 1414 / CC1/2: 0.917 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VOJ Resolution: 1.89→23.78 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4015 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: 14.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→23.78 Å
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Refine LS restraints |
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LS refinement shell |
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