+Open data
-Basic information
Entry | Database: PDB / ID: 2m9p | |||||||||
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Title | NMR structure of an inhibitor bound dengue NS3 protease | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / NS2B cofactor / covalent ligand / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / protein complex oligomerization / double-stranded RNA binding ...host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / protein complex oligomerization / double-stranded RNA binding / 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 / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 2 | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Model details | lowest energy, model7 | |||||||||
Authors | Gibbs, A. / Tounge, B. / Steele, R. | |||||||||
Citation | Journal: To be Published Title: NMR structure of an inhibitor bound dengue NS3 protease provides new insights into the NS2B NS3 ligand interactions Authors: Gibbs, A. / Tounge, B. / Steele, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m9p.cif.gz | 718.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m9p.ent.gz | 596.9 KB | Display | PDB format |
PDBx/mmJSON format | 2m9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/2m9p ftp://data.pdbj.org/pub/pdb/validation_reports/m9/2m9p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 25343.268 Da / Num. of mol.: 1 / Fragment: UNP residues 1391-1440 and 1476-1648 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Strain: Thailand/0168/1979 / Production host: Escherichia coli (E. coli) References: UniProt: P14337*PLUS, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase |
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#2: Protein/peptide | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Dengue NS3: One of two observed ligand binding modes | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8 mM [U-13C; U-15N; U-2H] protein, 0.8 mM [U-5% 13C; U-100% 15N] protein, 0.8 mM [U-13C; U-15N; U-2H];[1H-13C]-I(delta1)LVM protein, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |