[English] 日本語
Yorodumi- PDB-5i3p: DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO COMPOUND 27 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i3p | ||||||
---|---|---|---|---|---|---|---|
Title | DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO COMPOUND 27 | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE/INHIBITOR / polymerase / dengue / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...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 / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Noble, C.G. | ||||||
Citation | Journal: Plos Pathog. / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i3p.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i3p.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5i3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/5i3p ftp://data.pdbj.org/pub/pdb/validation_reports/i3/5i3p | HTTPS FTP |
---|
-Related structure data
Related structure data | 5i3qC 5jjrC 5jjsC 5k5mC 4hhjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 73624.867 Da / Num. of mol.: 1 Fragment: RNA-DEPENDENT RNA POLYMERASE, UNP RESIDUES 2762-3390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DLV0, UniProt: Q6YMS4*PLUS | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-68T / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.98 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS PH 8.0, 25% PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 17, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.45→88.06 Å / Num. obs: 30978 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Net I/σ(I): 14.4 | |||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HHJ Resolution: 2.45→31.48 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.324 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.221
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.89 Å2 / Biso mean: 49.96 Å2 / Biso min: 15.98 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.238 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.45→31.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.54 Å / Total num. of bins used: 15
|