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- PDB-8b07: Crystal structure of monkeypox virus methyltransferase VP39 in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b07 | ||||||
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Title | Crystal structure of monkeypox virus methyltransferase VP39 in complex with sinefungin | ||||||
![]() | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase | ||||||
![]() | VIRAL PROTEIN / viral / methyltransferase / vp39 / monkeypox / capping / enzyme | ||||||
Function / homology | ![]() regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silhan, J. / Klima, M. / Boura, E. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase. Authors: Silhan, J. / Klima, M. / Otava, T. / Skvara, P. / Chalupska, D. / Chalupsky, K. / Kozic, J. / Nencka, R. / Boura, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.8 KB | Display | ![]() |
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PDB format | ![]() | 106.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.4 KB | Display | ![]() |
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Full document | ![]() | 919.4 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ceqC ![]() 8cerC ![]() 8cesC ![]() 8cetC ![]() 8cevC ![]() 8cgbC ![]() 1vp3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 35949.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PAPS, MPXV-M2940_FCT-085, MPXV-M2957_Lagos-085, MPXV-M3021_Delta-085, MPXV-M5312_HM12_Rivers-085, MPXV-M5320_M15_Bayelsa-078, MPXV-Nig_SEV71_2_82-080, MPXV-Singapore-085, MPXV-UK_P1-085, MPXV- ...Gene: PAPS, MPXV-M2940_FCT-085, MPXV-M2957_Lagos-085, MPXV-M3021_Delta-085, MPXV-M5312_HM12_Rivers-085, MPXV-M5320_M15_Bayelsa-078, MPXV-Nig_SEV71_2_82-080, MPXV-Singapore-085, MPXV-UK_P1-085, MPXV-UK_P2-085, MPXV-UK_P3-085, MPXV-W_Nigeria-080, MPXV297957_076, MPXV298464_067, PDLMKLCO_00090 Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM lithium citrate, 14.5% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→49.17 Å / Num. obs: 43138 / % possible obs: 99.82 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2726 / Rpim(I) all: 0.07762 / Rrim(I) all: 0.2836 / Net I/σ(I): 9.82 |
Reflection shell | Resolution: 2.05→2.125 Å / Redundancy: 13.4 % / Rmerge(I) obs: 2.276 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4205 / CC1/2: 0.448 / CC star: 0.786 / Rpim(I) all: 0.6401 / Rrim(I) all: 2.366 / % possible all: 98.52 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VP3 Resolution: 2.05→49.17 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.989 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→49.17 Å
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Refine LS restraints |
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LS refinement shell |
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