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Open data
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Basic information
Entry | Database: PDB / ID: 5jjs | ||||||
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Title | Dengue 3 NS5 protein with compound 27 | ||||||
![]() | Genome polyprotein | ||||||
![]() | TRANSFERASE/INHIBITOR / RdRP / Dengue / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | ![]() symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / 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 / 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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lescar, J. / El Sahili, A. | ||||||
![]() | ![]() Title: Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling Authors: Lim, S.P. / Noble, C.G. / Seh, C.C. / Soh, T.S. / El Sahili, A. / Chan, G.K. / Lescar, J. / Arora, R. / Benson, T. / Nilar, S. / Manjunatha, U. / Wan, K.F. / Dong, H. / Xie, X. / Shi, P.Y. / Yokokawa, 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 | ![]() | 209.3 KB | Display | ![]() |
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PDB format | ![]() | 160.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 983.4 KB | Display | ![]() |
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Full document | ![]() | 990.2 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i3pC ![]() 5i3qC ![]() 5jjrC ![]() 5k5mC ![]() 4v0qS 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 102830.633 Da / Num. of mol.: 1 / Fragment: UNP residues 2494-3385 / Mutation: Q5M, V72I, G374E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 649 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/6L2.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/6L2.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-6L2 / | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-SAH / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium formate 1mM TCEP 18% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.49 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.13 |
Reflection shell | Resolution: 1.65→1.75 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4V0Q Resolution: 1.65→24.16 Å / Cor.coef. Fo:Fc: 0.9548 / Cor.coef. Fo:Fc free: 0.9443 / SU R Cruickshank DPI: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.083 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Displacement parameters | Biso mean: 27.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.172 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→24.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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