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- PDB-23ly: Crystal structure of SARS-CoV-2 main protease E166V mutant in com... -

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Entry
Database: PDB / ID: 23ly
TitleCrystal structure of SARS-CoV-2 main protease E166V mutant in complex with leritrelvir
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / SARS-CoV-2 / NSP5 / main protease / coronavirus / protease inhibitor / alpha-ketoamide inhibitor / peptidomimetic inhibitor
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / endonuclease 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 / methylation / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome ...viral genome replication / methyltransferase activity / endonuclease 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 / methylation / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding
Similarity search - Function
Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus Nsp6 transmembrane protein profile. ...Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-terminal / : / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, 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 Nsp3 ectodomain (3Ecto) 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 replicase NSP7 / 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
Chem-7ON / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsHuang, X. / Li, Q. / Yang, Z. / Zhong, N. / Xiong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82341085 China
CitationJournal: Biorxiv / Year: 2026
Title: Enhanced Target Binding by Leritrelvir Restores Dimerization of Mpro Mutants and Mitigates Drug Resistance
Authors: Huang, X. / Kuzmic, P. / Zhang, S. / Ramos-Guzman, C.A. / Chen, X. / Gui, J. / Li, Q. / Yan, S. / Zou, B. / Niu, C. / Zhao, Y. / Lin, H. / Wang, N. / Chen, J. / Chen, X. / Spencer, J. / ...Authors: Huang, X. / Kuzmic, P. / Zhang, S. / Ramos-Guzman, C.A. / Chen, X. / Gui, J. / Li, Q. / Yan, S. / Zou, B. / Niu, C. / Zhao, Y. / Lin, H. / Wang, N. / Chen, J. / Chen, X. / Spencer, J. / Mulholland, A.J. / Chen, J. / Zhong, N. / Yang, Z. / Xiong, X.
History
DepositionFeb 11, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9675
Polymers67,5912
Non-polymers1,3763
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-15 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.837, 106.317, 54.145
Angle α, β, γ (deg.)90.000, 103.218, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 1 - 306 / Label seq-ID: 1 - 306

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Global NCS restraints between domains: 1 2)

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Components

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


Mass: 33795.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-7ON / Leritrelvir bound form


Mass: 641.722 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C31H46F3N5O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Ammonium citrate tribasic pH 6.0, 14% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 8, 2024
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.56→53.16 Å / Num. obs: 76106 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.2
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3784 / CC1/2: 0.615

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSBUILT 20240630data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→53.159 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.141 / SU B: 5.226 / SU ML: 0.078 / Average fsc free: 0.9699 / Average fsc work: 0.986 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1974 3863 5.094 %
Rwork0.1475 71977 -
all0.15 --
obs-75840 99.355 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.353 Å2
Baniso -1Baniso -2Baniso -3
1-2.516 Å2-0 Å2-0.094 Å2
2--1.641 Å20 Å2
3----3.704 Å2
Refinement stepCycle: LAST / Resolution: 1.56→53.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 96 481 5279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124954
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164591
X-RAY DIFFRACTIONr_angle_refined_deg1.81.7946756
X-RAY DIFFRACTIONr_angle_other_deg0.6171.72810568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9135624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.7996.87532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92810768
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg3.319102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.51210217
X-RAY DIFFRACTIONr_chiral_restr0.0850.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021158
X-RAY DIFFRACTIONr_nbd_refined0.2190.2899
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.24377
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22493
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.22628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2304
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3430.223
X-RAY DIFFRACTIONr_nbd_other0.2140.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.220
X-RAY DIFFRACTIONr_mcbond_it5.9562.1262463
X-RAY DIFFRACTIONr_mcbond_other5.9382.1262463
X-RAY DIFFRACTIONr_mcangle_it8.8713.8233080
X-RAY DIFFRACTIONr_mcangle_other8.873.8243081
X-RAY DIFFRACTIONr_scbond_it7.1512.3822491
X-RAY DIFFRACTIONr_scbond_other7.1492.3822492
X-RAY DIFFRACTIONr_scangle_it10.4144.2533670
X-RAY DIFFRACTIONr_scangle_other10.4124.2533671
X-RAY DIFFRACTIONr_lrange_it16.75827.09821509
X-RAY DIFFRACTIONr_lrange_other15.70226.60821124
X-RAY DIFFRACTIONr_rigid_bond_restr3.60939545
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional; tight thermal / Rms dev Biso : 6.21523 Å2 / Rms dev position: 0.20977 Å / Weight Biso : 0.5 / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.56-1.60.262980.23253130.23456370.9560.97399.53880.207
1.6-1.6440.2522640.22152260.22255020.9570.97399.78190.192
1.644-1.6920.2712540.20950770.21253400.9430.97599.83150.175
1.692-1.7440.2332680.16948980.17251860.9670.98599.61430.138
1.744-1.8010.2172560.16547620.16850340.970.98699.68220.134
1.801-1.8640.232470.15545670.15948240.9670.98999.79270.125
1.864-1.9350.2362380.1544220.15446810.9660.9999.55140.121
1.935-2.0130.2082560.13841990.14245110.9780.99198.75860.112
2.013-2.1030.2162430.14940130.15343120.9710.98998.70130.124
2.103-2.2050.2082110.13338850.13741660.9760.99198.31970.114
2.205-2.3240.21850.12437330.12739420.9760.99299.39120.11
2.324-2.4650.1811800.1335360.13337300.980.99199.62470.12
2.465-2.6350.2071700.13233060.13634870.9750.99199.68450.125
2.635-2.8450.1971730.13731100.1433010.9760.98999.45470.135
2.845-3.1160.181450.13828200.1429850.9830.9999.330.141
3.116-3.4820.1951370.14825540.1527380.9780.98898.28340.154
3.482-4.0180.1371120.13422890.13524220.9860.9999.13290.15
4.018-4.9140.1511060.12219200.12320470.9880.99198.97410.144
4.914-6.920.199860.17414870.17515860.9850.98699.18030.201
6.92-53.1590.208340.168600.1629010.9770.98499.22310.192

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