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- PDB-6p6q: HCV NS3/4A protease domain of genotype 1a3a chimera in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p6q | ||||||
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Title | HCV NS3/4A protease domain of genotype 1a3a chimera in complex with grazoprevir | ||||||
![]() | Non-structural protein 4A,Serine protease NS3 | ||||||
![]() | VIRAL PROTEIN / Hydrolase / HCV NS3/4A protease HCV protease domain Grazoprevir / GZR Genotype 1a3a chimera | ||||||
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 / 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: Molecular mechanism of pan-genotypic HCV NS3/4A protease inhibition by glecaprevir and characterization of genotype-specific structural differences 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 | ![]() | 146 KB | Display | ![]() |
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PDB format | ![]() | 113.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p6rC ![]() 6p6sC ![]() 6p6tC ![]() 6p6vC ![]() 6p6zC ![]() 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21460.281 Da / Num. of mol.: 2 Mutation: C991S, V9941, V995N, L1013E, L1014E, I1017Q, I1018E, L1021Q, A1040T, C1047S, C1052L, I1072T, Q1080K, P1086Q, N1174S, C1159S, I1132L, D1168Q, R1123T 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, 65 molecules ![](data/chem/img/SUE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 0.1 M MES pH 6.5 5 % (NH4)2SO4 24 % PEG 3350 3 mM grazoprevir |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→48.954 Å / Num. obs: 9272 / % possible obs: 99.86 % / Redundancy: 2 % / Rmerge(I) obs: 0.0819 / Net I/σ(I): 7.18 |
Reflection shell | Resolution: 3.5→3.625 Å / Rmerge(I) obs: 0.1376 / Num. unique obs: 475 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5voj Resolution: 3.5→48.954 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→48.954 Å
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Refine LS restraints |
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LS refinement shell |
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