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Yorodumi- PDB-6p6v: HCV NS3/4A protease domain of genotype 5a in complex with glecaprevir -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p6v | ||||||
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Title | HCV NS3/4A protease domain of genotype 5a in complex with glecaprevir | ||||||
Components | Non-structural protein 4A,Serine protease NS3 | ||||||
Keywords | VIRAL PROTEIN / Hydrolase / HCV NS3/4A protease HCV protease domain Glecaprevir / GLE Genotype 1a3a chimera | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / 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 ...symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / 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 / protein complex oligomerization / monoatomic ion channel activity / SH3 domain binding / nucleoside-triphosphate phosphatase / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / 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 / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Hepatitis C virus genotype 5a | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Timm, J. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p6v.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p6v.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 6p6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p6v_validation.pdf.gz | 372.1 KB | Display | wwPDB validaton report |
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Full document | 6p6v_full_validation.pdf.gz | 375 KB | Display | |
Data in XML | 6p6v_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 6p6v_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/6p6v ftp://data.pdbj.org/pub/pdb/validation_reports/p6/6p6v | HTTPS FTP |
-Related structure data
Related structure data | 6p6qC 6p6rC 6p6sC 6p6tC 6p6zC 5vojS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 21370.412 Da / Num. of mol.: 1 / Mutation: V1040E, L1041E, I1044Q, I1045E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus genotype 5a (isolate SA13) Strain: isolate SA13 / Production host: Escherichia coli (E. coli) References: UniProt: O91936, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase |
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-Non-polymers , 5 types, 229 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-O31 / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M TMAO 0.1 M Tris pH 8.5 16% PEG 2000 MME 3 mM glecaprevir |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 3, 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: 2→22.814 Å / Num. obs: 13535 / % possible obs: 96.05 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 44.17 |
Reflection shell | Resolution: 2→2.072 Å / Rmerge(I) obs: 0.14 / Num. unique obs: 1289 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5voj Resolution: 2→22.814 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→22.814 Å
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Refine LS restraints |
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LS refinement shell |
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