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

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Basic information

Entry
Database: PDB / ID: 9uos
TitleCrystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 8
Components3C-like protease
KeywordsVIRAL PROTEIN / 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
: / ORF1ab polyprotein
Similarity search - Component
Biological speciesPorcine deltacoronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 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 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)206,70712
Polymers203,8366
Non-polymers2,8716
Water39622
1
A: 3C-like protease
D: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9024
Polymers67,9452
Non-polymers9572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-14 kcal/mol
Surface area23420 Å2
MethodPISA
2
B: 3C-like protease
E: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9024
Polymers67,9452
Non-polymers9572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-15 kcal/mol
Surface area23960 Å2
MethodPISA
3
C: 3C-like protease
hetero molecules

F: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9024
Polymers67,9452
Non-polymers9572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+y+1,-x,z-1/31
Buried area2100 Å2
ΔGint-9 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.820, 122.820, 290.907
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-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.: 6 / Source method: obtained synthetically / Formula: C21H33F3N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 60.42 %
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 EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.73→106.37 Å / Num. obs: 66061 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.41 / Rpim(I) all: 0.137 / Rrim(I) all: 0.433 / Χ2: 0.99 / Net I/σ(I): 5.5 / Num. measured all: 652724
Reflection shellResolution: 2.73→2.87 Å / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 4.912 / Num. measured all: 95396 / Num. unique obs: 9623 / CC1/2: 0.395 / Rpim(I) all: 1.63 / Rrim(I) all: 5.177 / Χ2: 0.97 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→61.41 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 3284 5.03 %
Rwork0.2227 --
obs0.2245 65325 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→61.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13558 0 198 22 13778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414089
X-RAY DIFFRACTIONf_angle_d0.61419292
X-RAY DIFFRACTIONf_dihedral_angle_d16.2994840
X-RAY DIFFRACTIONf_chiral_restr0.0452217
X-RAY DIFFRACTIONf_plane_restr0.0032471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.770.39011430.34442478X-RAY DIFFRACTION93
2.77-2.810.32521340.33872574X-RAY DIFFRACTION95
2.81-2.860.34331550.32392653X-RAY DIFFRACTION97
2.86-2.90.39291610.33242661X-RAY DIFFRACTION99
2.9-2.960.36861580.33282686X-RAY DIFFRACTION99
2.96-3.010.34041510.33742686X-RAY DIFFRACTION100
3.01-3.080.411470.31092746X-RAY DIFFRACTION100
3.08-3.140.32061470.2972680X-RAY DIFFRACTION100
3.14-3.220.33031320.30092740X-RAY DIFFRACTION100
3.22-3.30.30321200.29472716X-RAY DIFFRACTION100
3.3-3.390.32091540.2852727X-RAY DIFFRACTION100
3.39-3.480.32591550.25212707X-RAY DIFFRACTION100
3.48-3.60.26711330.23862754X-RAY DIFFRACTION100
3.6-3.730.24861660.22442709X-RAY DIFFRACTION100
3.73-3.880.32751180.21472719X-RAY DIFFRACTION100
3.88-4.050.25971040.19622764X-RAY DIFFRACTION100
4.05-4.260.22051360.18592739X-RAY DIFFRACTION100
4.26-4.530.19141580.16232726X-RAY DIFFRACTION100
4.53-4.880.18391480.16072705X-RAY DIFFRACTION100
4.88-5.370.18511530.17222718X-RAY DIFFRACTION100
5.37-6.150.24381480.20062751X-RAY DIFFRACTION100
6.15-7.750.22721390.19982725X-RAY DIFFRACTION100
7.75-61.410.19691240.17882677X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 43.2617 Å / Origin y: -17.279 Å / Origin z: 1.8561 Å
111213212223313233
T0.3879 Å2-0.0165 Å20.0298 Å2-0.3785 Å20.0149 Å2--0.3704 Å2
L0.868 °20.0141 °20.1153 °2-0.3584 °2-0.0191 °2--0.5163 °2
S-0.1253 Å °-0.0062 Å °-0.1841 Å °0.0395 Å °0.0107 Å °-0.1532 Å °0.0121 Å °0.1463 Å °0.1159 Å °
Refinement TLS groupSelection details: all

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