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Yorodumi- PDB-5nh0: Structure of human coronavirus NL63 main protease in complex with... -
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-Basic information
Entry | Database: PDB / ID: 5nh0 | |||||||||
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Title | Structure of human coronavirus NL63 main protease in complex with the alpha-ketoamide tert-Butyl ((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)b- utan-2-yl)carbamate (tert-butyl -GlnLactam-CO-CO-NH-benzyl) | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | HYDROLASE / Viral protease / coronavirus / alpha-ketoamide / inhibitor | |||||||||
Function / homology | Function and homology information host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / 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 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Human coronavirus NL63 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Zhang, L. / Hilgenfeld, R. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication Authors: Lin, D. / Zhang, L. / Kusov, Y. / Nian, Y. / Ma, Q. / Wang, J. / Leyssen, P. / Lanko, K. / Neyts, J. / de Wilde, A. / Snijder, E.J. / Liu, H. / Hilgenfeld, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nh0.cif.gz | 194.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nh0.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 5nh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nh0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5nh0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5nh0_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 5nh0_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/5nh0 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/5nh0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 32407.740 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus NL63 / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0C6X5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M lithium sulfate monohydrate, 0.1 M sodium citrate tribasic dihydrate, 25% PEG 1,000, pH 6.0 PH range: 4.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→44.28 Å / Num. obs: 68423 / % possible obs: 98.2 % / Redundancy: 4.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.038 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3 / Num. unique obs: 9796 / CC1/2: 0.873 / Rpim(I) all: 0.25 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HCoV-NL63 main protease Resolution: 2.35→42.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.139 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.189 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.818 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→42.89 Å
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Refine LS restraints |
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