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- PDB-9uor: Crystal structure of IBV 3CL protease (3CLpro) in complex with co... -

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Basic information

Entry
Database: PDB / ID: 9uor
TitleCrystal structure of IBV 3CL protease (3CLpro) in complex with compound 8
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Mpro / VIRAL PROTEIN-inhibitor complex
Function / homology
Function and homology information


viral genome replication / transferase activity / omega peptidase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of autophagy / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane ...viral genome replication / transferase activity / omega peptidase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of autophagy / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Papain-like viral protease, palm and finger domains, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus ...Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Papain-like viral protease, palm and finger domains, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / : / : / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Replicase polyprotein 1a
Similarity search - Component
Biological speciesAvian infectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNie, T.Q. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2025
Title: Structure-Based Development of Ultra-Broad-Spectrum 3C-Like Protease Inhibitors.
Authors: Su, H. / Nie, T. / Chen, G. / Xiong, M. / Zhang, Y. / Wu, G. / You, M. / Xie, H. / He, J. / Xiong, Y. / Hu, H. / Zhao, W. / Li, M. / Xiao, G. / Zhang, L. / Xu, Y.
History
DepositionApr 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9554
Polymers66,9982
Non-polymers9572
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-13 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.297, 94.690, 71.449
Angle α, β, γ (deg.)90.00, 112.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / p33


Mass: 33498.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian infectious bronchitis virus (strain Beaudette)
Gene: 1a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0C6V3, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-A1EPZ / (2~{S})-2-[[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]amino]-4-methyl-~{N}-[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]pentanamide


Type: peptide-like / Mass: 478.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H33F3N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG3350, 100 mM BIS-TRIS propane, pH 7.5, 200 mM potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.6→34.68 Å / Num. obs: 89675 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Χ2: 0.8 / Net I/σ(I): 11.3 / Num. measured all: 573463
Reflection shellResolution: 1.6→1.64 Å / % possible obs: 100 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.974 / Num. measured all: 33644 / Num. unique obs: 6603 / CC1/2: 0.624 / Rpim(I) all: 0.486 / Rrim(I) all: 1.093 / Χ2: 0.72 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.33 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 4177 4.67 %
Rwork0.2019 --
obs0.2032 89496 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 66 419 5050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144737
X-RAY DIFFRACTIONf_angle_d1.3426472
X-RAY DIFFRACTIONf_dihedral_angle_d7.114677
X-RAY DIFFRACTIONf_chiral_restr0.088748
X-RAY DIFFRACTIONf_plane_restr0.012827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.29831320.27622752X-RAY DIFFRACTION96
1.62-1.640.29521150.26842856X-RAY DIFFRACTION100
1.64-1.660.26641380.25242835X-RAY DIFFRACTION100
1.66-1.680.26921230.2452847X-RAY DIFFRACTION100
1.68-1.70.26731390.23582839X-RAY DIFFRACTION100
1.7-1.720.21181300.22342837X-RAY DIFFRACTION100
1.72-1.750.23311280.21422866X-RAY DIFFRACTION100
1.75-1.770.25221410.21922825X-RAY DIFFRACTION100
1.77-1.80.27261560.22752830X-RAY DIFFRACTION100
1.8-1.830.28611320.23872848X-RAY DIFFRACTION100
1.83-1.860.27711430.23742819X-RAY DIFFRACTION100
1.86-1.90.27251150.22412855X-RAY DIFFRACTION100
1.9-1.930.2041390.212824X-RAY DIFFRACTION100
1.93-1.970.22271650.20872843X-RAY DIFFRACTION100
1.97-2.010.24591660.21412778X-RAY DIFFRACTION100
2.01-2.060.23841630.20592840X-RAY DIFFRACTION100
2.06-2.110.23321370.21242868X-RAY DIFFRACTION100
2.11-2.170.24551540.21652822X-RAY DIFFRACTION100
2.17-2.230.26961230.21432837X-RAY DIFFRACTION100
2.23-2.310.24291450.2132864X-RAY DIFFRACTION100
2.31-2.390.2951380.22132841X-RAY DIFFRACTION100
2.39-2.480.25141460.21262832X-RAY DIFFRACTION100
2.48-2.60.24941170.212876X-RAY DIFFRACTION100
2.6-2.730.22311480.2072852X-RAY DIFFRACTION100
2.73-2.90.23781470.20482852X-RAY DIFFRACTION100
2.91-3.130.22031280.19952878X-RAY DIFFRACTION100
3.13-3.440.24451310.19992858X-RAY DIFFRACTION100
3.44-3.940.19821360.17642893X-RAY DIFFRACTION100
3.94-4.960.15331430.15252850X-RAY DIFFRACTION100
4.96-34.330.20351590.18022902X-RAY DIFFRACTION100

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