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- PDB-9x7d: Crystal structure of PDCoV 3CL protease (3CLpro) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9x7d
TitleCrystal structure of PDCoV 3CL protease (3CLpro) in complex with nirmatrelvir
Components3C-like protease
KeywordsVIRAL PROTEIN / Protease / Mpro / Viral protein-inhibitor complex
Function / homology
Function and homology information


host cell membrane / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / omega peptidase activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / viral protein processing ...host cell membrane / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / omega peptidase activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / AAA domain / NSP15, NendoU domain, coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus ...Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / AAA domain / NSP15, NendoU domain, coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / : / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-4WI / ORF1ab polyprotein
Similarity search - Component
Biological speciesPorcine deltacoronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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
DepositionOct 16, 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 protease
B: 3C-like protease
C: 3C-like protease
D: 3C-like protease
E: 3C-like protease
F: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,84512
Polymers203,8366
Non-polymers3,0096
Water3,135174
1
A: 3C-like protease
E: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9484
Polymers67,9452
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-12 kcal/mol
Surface area23920 Å2
MethodPISA
2
B: 3C-like protease
D: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9484
Polymers67,9452
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-12 kcal/mol
Surface area24110 Å2
MethodPISA
3
C: 3C-like protease
hetero molecules

F: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9484
Polymers67,9452
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_444-x+y-1,-x-1,z-1/31
Buried area2370 Å2
ΔGint-10 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.521, 122.521, 292.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
3C-like protease


Mass: 33972.641 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine deltacoronavirus / Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A166XB12
#2: Chemical
ChemComp-4WI / (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide / PF-07321332, bound form / nirmatrelvir, bound form / Paxlovid, bound form


Mass: 501.542 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H34F3N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.5-2% PEG6000, 100 mM sodium citrate, pH 4.6-5.25

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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 EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.28→106.11 Å / Num. obs: 109059 / % possible obs: 96.6 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.031 / Rrim(I) all: 0.098 / Χ2: 0.91 / Net I/σ(I): 17.8 / Num. measured all: 1113142
Reflection shellResolution: 2.28→2.4 Å / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 1.419 / Num. measured all: 172359 / Num. unique obs: 16449 / CC1/2: 0.867 / Rpim(I) all: 0.457 / Rrim(I) all: 1.491 / Χ2: 0.82 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→61.26 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 5361 4.93 %
Rwork0.2082 --
obs0.2101 108819 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→61.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13713 0 210 174 14097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314270
X-RAY DIFFRACTIONf_angle_d0.5719543
X-RAY DIFFRACTIONf_dihedral_angle_d16.3164983
X-RAY DIFFRACTIONf_chiral_restr0.0452233
X-RAY DIFFRACTIONf_plane_restr0.0042498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.30.33772240.313504X-RAY DIFFRACTION99
2.3-2.330.36091470.30013588X-RAY DIFFRACTION100
2.33-2.360.38322000.29563571X-RAY DIFFRACTION99
2.36-2.390.34581810.28853533X-RAY DIFFRACTION99
2.39-2.420.3471980.27933545X-RAY DIFFRACTION100
2.42-2.450.32261780.27773601X-RAY DIFFRACTION99
2.45-2.490.31921830.27033495X-RAY DIFFRACTION99
2.49-2.530.31861780.25813581X-RAY DIFFRACTION99
2.53-2.560.29251850.25683506X-RAY DIFFRACTION99
2.56-2.610.30641810.25463599X-RAY DIFFRACTION100
2.61-2.650.30831710.25663535X-RAY DIFFRACTION99
2.65-2.70.3322880.25421731X-RAY DIFFRACTION49
2.7-2.750.30911980.24253567X-RAY DIFFRACTION100
2.75-2.810.30611880.24423548X-RAY DIFFRACTION100
2.81-2.870.29031850.2453607X-RAY DIFFRACTION100
2.87-2.940.29571740.2483556X-RAY DIFFRACTION100
2.94-3.010.28581770.24393589X-RAY DIFFRACTION100
3.01-3.090.26851840.24613570X-RAY DIFFRACTION100
3.09-3.180.27821970.23993533X-RAY DIFFRACTION100
3.18-3.280.28451850.2493600X-RAY DIFFRACTION100
3.28-3.40.33471990.24243601X-RAY DIFFRACTION100
3.4-3.540.24572070.22082786X-RAY DIFFRACTION80
3.54-3.70.25481550.21843048X-RAY DIFFRACTION85
3.7-3.880.2281660.20073342X-RAY DIFFRACTION99
3.91-4.140.2261650.17993399X-RAY DIFFRACTION100
4.14-4.460.21721700.16513591X-RAY DIFFRACTION100
4.46-4.90.15151650.15683628X-RAY DIFFRACTION100
4.91-5.610.22461780.16673577X-RAY DIFFRACTION100
5.62-7.070.18631780.18583606X-RAY DIFFRACTION100
7.07-61.260.1981760.1583521X-RAY DIFFRACTION97

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