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- PDB-4nrt: Human Norovirus polymerase bound to Compound 6 (suramin derivative) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nrt | ||||||
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Title | Human Norovirus polymerase bound to Compound 6 (suramin derivative) | ||||||
![]() | hNV-RdRp | ||||||
![]() | VIRAL PROTEIN/TRANSCRIPTION INHIBITOR / RNA dependent RNA Polymerase / VIRAL PROTEIN-TRANSCRIPTION INHIBITOR complex | ||||||
Function / homology | ![]() calicivirin / RNA-protein covalent cross-linking / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Croci, R. / Pezzullo, M. / Tarantino, D. / Mastrangelo, E. / Milani, M. / Bolognesi, M. | ||||||
![]() | ![]() Title: Structural bases of norovirus RNA dependent RNA polymerase inhibition by novel suramin-related compounds. Authors: Croci, R. / Pezzullo, M. / Tarantino, D. / Milani, M. / Tsay, S.C. / Sureshbabu, R. / Tsai, Y.J. / Mastrangelo, E. / Rohayem, J. / Bolognesi, M. / Hwu, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.7 KB | Display | ![]() |
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PDB format | ![]() | 93.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.3 KB | Display | ![]() |
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Full document | ![]() | 731.4 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nruC ![]() 2b43S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 58657.762 Da / Num. of mol.: 1 Fragment: RNA dependent RNA polymerase (UNP Residues 1190-1699) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-2NG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 1.2 M Na Citrate, 100 mM Na Cacodylate ph 6.2, 125 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2013 |
Radiation | Monochromator: Si[111] CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→71.8 Å / Num. obs: 39356 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.02→2.13 Å / Rmerge(I) obs: 0.305 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B43 Resolution: 2.022→69.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.022→69.85 Å
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Refine LS restraints |
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