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- PDB-9x7h: Crystal structure of PDCoV 3CL protease (3CLpro) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9x7h
TitleCrystal structure of PDCoV 3CL protease (3CLpro) in complex with compound 6
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 / lyase activity ...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 / lyase activity / viral protein processing / host cell perinuclear region of cytoplasm / symbiont-mediated activation of host autophagy / viral translational frameshifting / 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: 2.56 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)206,59312
Polymers203,8366
Non-polymers2,7586
Water2,018112
1
A: 3C-like protease
hetero molecules

B: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8644
Polymers67,9452
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area2730 Å2
ΔGint-12 kcal/mol
Surface area24360 Å2
MethodPISA
2
C: 3C-like protease
D: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8644
Polymers67,9452
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-8 kcal/mol
Surface area24680 Å2
MethodPISA
3
E: 3C-like protease
F: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8644
Polymers67,9452
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-15 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.926, 122.926, 291.591
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-A1D7M / (2~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-2-[[(2~{S})-3,3-dimethyl-2-(methylsulfonylamino)butanoyl]amino]-4-methyl-pentanamide


Type: peptide-like / Mass: 459.603 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H37N5O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
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: Jul 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.56→106.46 Å / Num. obs: 79964 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.044 / Rrim(I) all: 0.136 / Χ2: 0.98 / Net I/σ(I): 15.8 / Num. measured all: 757448
Reflection shellResolution: 2.56→2.7 Å / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 1.538 / Num. measured all: 112813 / Num. unique obs: 11606 / CC1/2: 0.837 / Rpim(I) all: 0.518 / Rrim(I) all: 1.624 / Χ2: 0.91 / Net I/σ(I) obs: 2.7

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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: 2.56→53.23 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 4046 5.07 %
Rwork0.1983 --
obs0.2007 79748 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→53.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13866 0 186 112 14164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314393
X-RAY DIFFRACTIONf_angle_d0.60219649
X-RAY DIFFRACTIONf_dihedral_angle_d17.6615072
X-RAY DIFFRACTIONf_chiral_restr0.0472220
X-RAY DIFFRACTIONf_plane_restr0.0032511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.590.38941460.32142542X-RAY DIFFRACTION100
2.59-2.620.38131190.30412660X-RAY DIFFRACTION99
2.62-2.650.35311310.30072589X-RAY DIFFRACTION100
2.65-2.690.37031190.28742626X-RAY DIFFRACTION100
2.69-2.730.33441390.27652622X-RAY DIFFRACTION100
2.73-2.770.36671310.27372586X-RAY DIFFRACTION100
2.77-2.810.34441340.2682644X-RAY DIFFRACTION100
2.81-2.850.34311410.26772596X-RAY DIFFRACTION100
2.85-2.90.33841230.27182588X-RAY DIFFRACTION100
2.9-2.950.32631690.25932590X-RAY DIFFRACTION100
2.95-30.32561460.24752646X-RAY DIFFRACTION100
3-3.060.28131250.24592592X-RAY DIFFRACTION100
3.06-3.120.29121310.24962619X-RAY DIFFRACTION100
3.12-3.190.33521450.2562603X-RAY DIFFRACTION100
3.19-3.260.32411040.23792636X-RAY DIFFRACTION100
3.26-3.340.30681530.2392592X-RAY DIFFRACTION100
3.34-3.430.28851580.22122624X-RAY DIFFRACTION100
3.44-3.540.28281640.21472566X-RAY DIFFRACTION100
3.54-3.650.24921190.21582637X-RAY DIFFRACTION100
3.65-3.780.23341760.20552563X-RAY DIFFRACTION100
3.78-3.930.24291230.18592652X-RAY DIFFRACTION100
3.93-4.110.22671560.17212626X-RAY DIFFRACTION100
4.11-4.330.21121480.15782583X-RAY DIFFRACTION100
4.33-4.60.18071370.14722622X-RAY DIFFRACTION100
4.6-4.950.20181410.14962629X-RAY DIFFRACTION100
4.95-5.450.18091400.15562613X-RAY DIFFRACTION100
5.45-6.240.21341620.18062605X-RAY DIFFRACTION100
6.24-7.850.171280.17212633X-RAY DIFFRACTION100
7.86-53.230.16471380.14482618X-RAY DIFFRACTION98

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