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- PDB-8e7n: Crystal structure of beluga whale Gammacoronavirus SW1 Mpro with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e7n | ||||||
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Title | Crystal structure of beluga whale Gammacoronavirus SW1 Mpro with GC-376 captured in two conformational states | ||||||
![]() | main protease | ||||||
![]() | VIRAL PROTEIN / Gammacoronavirus / PROTEASE / DRUG RESISTANCE / COMPLEX / HYDROLASE / DURG DISCOVERY / MAIN PROTEASE / MPRO / SUBSTRATE COMPLEX / GC-376 / VIRAL PROTEIN-HYDROLASE-INHIBITOR complex / SW1 / Beluga Whale / Whale | ||||||
Function / homology | ![]() endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / omega peptidase activity / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm ...endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / omega peptidase activity / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shaqra, A.M. / Schiffer, C.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses. Authors: Zvornicanin, S.N. / Shaqra, A.M. / Huang, Q.J. / Ornelas, E. / Moghe, M. / Knapp, M. / Moquin, S. / Dovala, D. / Schiffer, C.A. / Kurt Yilmaz, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 115.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dsuC ![]() 8e7cC ![]() 8fwxC 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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Unit cell |
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Components
#1: Protein | Mass: 33512.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.71 Å3/Da / Density % sol: 54.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10-20 % (w/v) PEG 3350, 0.20-0.30 M NaCl, and 0.1 M Bis-Tris methane pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→12.24 Å / Num. obs: 81531 / % possible obs: 94.95 % / Redundancy: 2.4 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05568 / Rpim(I) all: 0.03864 / Rrim(I) all: 0.06827 / Net I/σ(I): 11.31 |
Reflection shell | Resolution: 1.65→1.709 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4862 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7698 / CC1/2: 0.735 / CC star: 0.921 / Rpim(I) all: 0.3696 / Rrim(I) all: 0.6148 / % possible all: 90.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Not submitted Resolution: 1.65→12.24 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3908 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→12.24 Å
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Refine LS restraints |
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LS refinement shell |
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