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- PDB-5trj: CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5trj | ||||||
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Title | CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 2-{[2-(carboxymethoxy)benzene-1-carbonyl]amino}-3-[(4-chlorophenyl)methoxy]benzoic acid | ||||||
![]() | RNA-DEPENDENT RNA POLYMERASE | ||||||
![]() | TRANSFERASE/TRANSFERASE inhibitor / NS5B / POLYMERASE / HCV / FINGERS / PALM / THUMB / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
Function / homology | ![]() positive stranded viral RNA replication / 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 / viral genome replication ...positive stranded viral RNA replication / 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 / viral genome replication / 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 / protein-containing complex / proteolysis / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sheriff, S. | ||||||
![]() | ![]() Title: Discovery and initial optimization of alkoxyanthranilic acid derivatives as inhibitors of HCV NS5B polymerase. Authors: Parcella, K. / Nickel, A. / Beno, B.R. / Sheriff, S. / Wan, C. / Wang, Y.K. / Roberts, S.B. / Meanwell, N.A. / Kadow, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.8 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 39.4 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5trhC ![]() 5triC ![]() 5trkC ![]() 3qoz C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 63961.516 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2992 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 100 mM Sodium Citrate, 1.75 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. obs: 40796 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 44.69 Å2 / Rsym value: 0.076 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.277 / % possible all: 59.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QOZ ![]() 3qoz Resolution: 2.57→33.89 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.881 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.731 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.734 / SU Rfree Blow DPI: 0.291 / SU Rfree Cruickshank DPI: 0.293
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Displacement parameters | Biso mean: 33.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→33.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.57→2.64 Å / Total num. of bins used: 20
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