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- PDB-8dmd: Room temperature X-ray structure of SARS-CoV-2 main protease in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dmd | ||||||
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Title | Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound ZZ4461624291 | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE/INHIBITOR / viral cysteine protease / homodimer / enzyme-inhibitor complex / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kovalevsky, A. / Coates, L. / Kneller, D.W. | ||||||
Funding support | 1items
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![]() | ![]() Title: AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. Authors: Joshi, R.P. / Schultz, K.J. / Wilson, J.W. / Kruel, A. / Varikoti, R.A. / Kombala, C.J. / Kneller, D.W. / Galanie, S. / Phillips, G. / Zhang, Q. / Coates, L. / Parvathareddy, J. / ...Authors: Joshi, R.P. / Schultz, K.J. / Wilson, J.W. / Kruel, A. / Varikoti, R.A. / Kombala, C.J. / Kneller, D.W. / Galanie, S. / Phillips, G. / Zhang, Q. / Coates, L. / Parvathareddy, J. / Surendranathan, S. / Kong, Y. / Clyde, A. / Ramanathan, A. / Jonsson, C.B. / Brandvold, K.R. / Zhou, M. / Head, M.S. / Kovalevsky, A. / Kumar, 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 | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 54.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 764 KB | Display | ![]() |
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Full document | ![]() | 764.9 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dl9C ![]() 8dlbC ![]() 6wqfS C: citing same article ( S: Starting model for refinement |
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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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-SVL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.44 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 17-22% PEG3350, 0.1 M Bis-Tris pH 6.5, microseeding |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.48 Å / Num. obs: 18551 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.911 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.039 / Net I/σ(I): 14.02 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1834 / CC1/2: 0.588 / Rpim(I) all: 0.33 / % possible all: 58.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WQF Resolution: 2→22.29 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→22.29 Å
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Refine LS restraints |
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LS refinement shell |
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