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- PDB-1dxw: structure of hetero complex of non structural protein (NS) of hep... -
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Basic information
Entry | Database: PDB / ID: 1dxw | ||||||
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Title | structure of hetero complex of non structural protein (NS) of hepatitis C virus (HCV) and synthetic peptidic compound | ||||||
![]() | SERINE PROTEASE | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / NON STRUCTURAL PROTEIN / HEPATITIS C VIRUS / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() host cell lipid droplet / transformation of host cell by virus / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid ...host cell lipid droplet / transformation of host cell by virus / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / lipid droplet / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont entry into host cell / 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 / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Barbato, G. / Cicero, D.O. / Cordier, F. / Narjes, F. / Gerlach, B. / Sambucini, S. / Grzesiek, S. / Matassa, V.G. / Defrancesco, R. / Bazzo, R. | ||||||
![]() | ![]() Title: Inhibitor Binding Induces Active Site Stabilisation of the Hcv Ns3 Protein Serine Protease Domain Authors: Barbato, G. / Cicero, D.O. / Cordier, F. / Narjes, F. / Gerlach, B. / Sambucini, S. / Grzesiek, S. / Matassa, V.G. / Defrancesco, R. / Bazzo, R. #1: ![]() Title: The Solution Structure of the N-Terminal Serine Protease Domain of the Hepatitis C Virus Ns3 Protein Provides New Insights Into its Activation and Catalytic Mechanism Authors: Barbato, G. / Cicero, D.O. / Nardi, M.C. / Steinkuhler, C. / Cortese, R. / Defrancesco, R. / Bazzo, R. #2: Journal: J.Mol.Biol. / Year: 1999 Title: Structural Characterization of the Interactions of Optimized Product Inhibitors with the N-Terminal Proteinase Domain of the Hepatitis C Virus (Hcv) Ns3 Protein by NMR and Modelling Studies Authors: Cicero, D.O. / Barbato, G. / Koch, U. / Ingallinella, P. / Bianchi, E. / Nardi, M.C. / Steinkuhler, C. / Cortese, R. / Matassa, V. / Defrancesco, R. / Pessi, A. / Bazzo, R. #3: Journal: J.Biol.Chem. / Year: 1998 Title: The Metal Binding Site of the Hepatitis C Virus Ns3 Protease Authors: Urbani, A. / Bazzo, R. / Nardi, M.C. / Cicero, D.O. / Defrancesco, R. / Steinkuhler, C. / Barbato, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 979.5 KB | Display | ![]() |
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PDB format | ![]() | 843.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 493.6 KB | Display | ![]() |
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Full document | ![]() | 695.2 KB | Display | |
Data in XML | ![]() | 94 KB | Display | |
Data in CIF | ![]() | 111.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 19634.529 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 1027-1206 Source method: isolated from a genetically manipulated source Details: COVALENT BOND BETWEEN SER 139 OG AND ABK 190 C1 (DI-FLUORO-ABU-KETOACID) OF INHIBITOR Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-2ZF / |
#3: Chemical | ChemComp-ZN / |
Sequence details | 6 RESIDUES INSERTED AT THE C TERMINAL (ALA SER LYS LYS LYS LYS) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE EXPERIMENTS, 3D HETERONUCLEAR NOESY EXPERIMENTS, 3D AND 2D COUPLING CONSTANT MEASUREMENTS, 10% GLUCOSE C13 LABELLING FOR METHYL ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE EXPERIMENTS, 3D HETERONUCLEAR NOESY EXPERIMENTS, 3D AND 2D COUPLING CONSTANT MEASUREMENTS, 10% GLUCOSE C13 LABELLING FOR METHYL STEREOSPECIFIC ASSINGMENT, COMBINED USE OF SEVERAL COUPLING CONSTANTS AND ROESY SPECTROSCOPY TO DETERMINE CHI1 ANGLES. |
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Sample preparation
Details | Contents: 95% WATER/10 % D2O |
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Sample conditions | pH: 6.6 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RESIDUES OF NS3 1-21 ARE NOT INCLUDED IN THE MODELS SINCE THEY ARE AFFECTED BY MOBILITY IN SOLUTION. | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20 |