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- PDB-4twy: Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)... -
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Basic information
Entry | Database: PDB / ID: 4twy | ||||||
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Title | Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor | ||||||
![]() | 3C-like proteinase | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / hydrase proteinase converting / designed inhibitor / hydrase-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / viral transcription / SARS-CoV-1 modulates host translation machinery ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / viral transcription / SARS-CoV-1 modulates host translation machinery / Transferases; Transferring one-carbon groups; Methyltransferases / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / 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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 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 / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Akaji, K. / Teruya, K. / Shimamoto, Y. / Sanjho, A. / Yamashita, E. / Nakagawa, A. | ||||||
![]() | ![]() Title: Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors Authors: Shimamoto, Y. / Hattori, Y. / Kobayashi, K. / Teruya, K. / Sanjoh, A. / Nakagawa, A. / Yamashita, E. / Akaji, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 79.4 KB | Display | ![]() |
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PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4twwC ![]() 4wy3C ![]() 3atwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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 on special symmetry positions |
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Details | 1 |
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Components
#1: Protein | Mass: 33832.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Akaji K, Konno H, Mitsui H, Teruya K , Shimamoto Y, Hattori Y, Ozaki T, Kusunoki M, Sanjoh A.Structure-Based Design, Synthesis, and Evaluation of Peptide-mimetic SARS 3CL Protease Inhibitors. ...Details: Akaji K, Konno H, Mitsui H, Teruya K , Shimamoto Y, Hattori Y, Ozaki T, Kusunoki M, Sanjoh A.Structure-Based Design, Synthesis, and Evaluation of Peptide-mimetic SARS 3CL Protease Inhibitors.Journal of Medicinal Chemistry 54, 7962-7973, 2011. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0C6X7, SARS coronavirus main proteinase |
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#2: Chemical | ChemComp-3BL / ( |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION ID NP_828863, WHICH IS NOT AVAILABLE FROM ...THE SEQUENCE HAS BEEN DEPOSITED TO GENBANK WITH ACCESSION ID NP_828863, WHICH IS NOT AVAILABLE FROM UNIPROT AT PRESENT. RESIDUE 188 IS ARG ACCORDING TO THE DATABASE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10%(w/v) of PEG20000, 100mM MES, 5mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 17, 2013 / Details: horizontal focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 57490 / % possible obs: 97 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.076 / Χ2: 1.32 / Net I/av σ(I): 21.878 / Net I/σ(I): 10.5 / Num. measured all: 239434 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ATW Resolution: 1.6→25.33 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.63 Å2 / Biso mean: 40.804 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 1.6→25.33 Å
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LS refinement shell | Resolution: 1.598→1.64 Å
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