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- PDB-6p6l: HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p6l | ||||||
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Title | HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir | ||||||
![]() | Non-structural protein 4A,Serine protease NS3 | ||||||
![]() | VIRAL PROTEIN / Hydrolase / HCV NS3/4A protease HCV protease domain Glecaprevir / GLE Genotype 1a | ||||||
Function / homology | ![]() hepacivirin / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / host cell nucleus / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Timm, J. / Schiffer, C.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: HCV NS3/4A protease domain of genotype 1a in complex with glecaprevir Authors: Timm, J. / Kosovrasti, K. / Henes, M. / Leidner, F. / Hou, S. / 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 | ![]() | 101.7 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p6mC ![]() 6p6oC ![]() 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: 21503.330 Da / Num. of mol.: 1 Mutation: L1013E, L1014E, I1017Q, I1018E, L1021Q, A1040T , C1047S, C1052L, I1072T, Q1080K , P1086Q, N1174S, C1159S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate 1 / Production host: ![]() ![]() References: UniProt: P26664, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase |
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-Non-polymers , 5 types, 294 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/O31.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/O31.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-O31 / ( | #6: 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: 45.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5 2% (NH4)2SO4 20% PEG 3350 / Temp details: room temperature |
-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: Mar 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.728→26.359 Å / Num. obs: 19501 / % possible obs: 92.56 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 37.76 |
Reflection shell | Resolution: 1.728→1.79 Å / Rmerge(I) obs: 0.18 / Num. unique obs: 1601 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5voj Resolution: 1.728→26.359 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.728→26.359 Å
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Refine LS restraints |
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LS refinement shell |
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