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- PDB-9rj8: SARS-CoV-2 with a bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 9rj8
TitleSARS-CoV-2 with a bound inhibitor
Components3C-like proteinase nsp5
KeywordsHYDROLASE / protease / inhibitor
Function / homology
Function and homology information


viral genome replication / methyltransferase 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 / 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 ...viral genome replication / methyltransferase 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 / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / 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 / membrane
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 / Carbamoyl-phosphate synthase subdomain signature 2. ...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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-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 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 speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.433 Å
AuthorsMac Sweeney, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SARS-CoV-2 with a bound inhibitor
Authors: Mac Sweeney, A.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 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 nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4744
Polymers67,6512
Non-polymers8232
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-10 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.802, 101.812, 103.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 301 / Label seq-ID: 1 - 301

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints 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: 33825.547 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 (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-A1JGT / 4-fluoranyl-~{N}-(3-phenoxypropyl)-~{N}-(1,2-thiazol-5-ylmethyl)-2,3-dihydroindole-1-carboxamide


Mass: 411.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22FN3O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES-imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.433→72.735 Å / Num. obs: 98276 / % possible obs: 94.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Net I/σ(I): 13
Reflection shellResolution: 1.433→1.543 Å / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4914 / CC1/2: 0.584 / Rpim(I) all: 0.441

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.433→72.735 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.529 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2168 4952 5.039 %
Rwork0.1594 93324 -
all0.162 --
obs-98276 74.275 %
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: 28.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.687 Å20 Å2-0 Å2
2---0.793 Å2-0 Å2
3---0.107 Å2
Refinement stepCycle: LAST / Resolution: 1.433→72.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 58 410 5107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124824
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164277
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6456561
X-RAY DIFFRACTIONr_angle_other_deg0.5321.5719971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.718520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69710762
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.12210211
X-RAY DIFFRACTIONr_chiral_restr0.0750.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02961
X-RAY DIFFRACTIONr_nbd_refined0.2060.2919
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.24173
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22349
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0960.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.210
X-RAY DIFFRACTIONr_nbd_other0.1530.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.224
X-RAY DIFFRACTIONr_mcbond_it5.8952.8962434
X-RAY DIFFRACTIONr_mcbond_other5.8772.8932431
X-RAY DIFFRACTIONr_mcangle_it6.8464.3463040
X-RAY DIFFRACTIONr_mcangle_other6.8474.3483041
X-RAY DIFFRACTIONr_scbond_it7.3553.342390
X-RAY DIFFRACTIONr_scbond_other7.3533.3412391
X-RAY DIFFRACTIONr_scangle_it7.724.8223520
X-RAY DIFFRACTIONr_scangle_other7.724.8233521
X-RAY DIFFRACTIONr_lrange_it7.86343.1765379
X-RAY DIFFRACTIONr_lrange_other7.81640.2585286
X-RAY DIFFRACTIONr_rigid_bond_restr8.91939101
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.059188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.116760.05008
12AX-RAY DIFFRACTIONLocal ncs0.116760.05008
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
1.433-1.470.294290.2876510.28796860.9480.9457.02040.279
1.47-1.5110.3271060.23719310.24294520.9410.96221.5510.223
1.511-1.5540.2841500.2328960.23391920.9460.96633.13750.21
1.554-1.6020.2421850.21739050.21889030.9620.9745.93960.195
1.602-1.6550.2573290.20650370.20987040.9580.97361.64980.179
1.655-1.7130.2483010.18559820.18883310.960.97875.41710.152
1.713-1.7770.2363530.1868920.18380980.9650.97989.46650.144
1.777-1.850.2413580.16472960.16778030.9660.98398.09050.131
1.85-1.9320.2424520.15769890.16274740.9660.98599.55850.13
1.932-2.0260.2133590.14467770.14871690.9750.98799.53970.125
2.026-2.1360.2133350.14464720.14868350.9740.98899.59030.131
2.136-2.2650.2223090.1461600.14464880.970.98899.70720.132
2.265-2.4220.2212860.13557690.13960850.9670.98999.5070.133
2.422-2.6150.2112690.1454070.14456880.9720.98899.7890.143
2.615-2.8650.2032580.14449720.14752370.9740.98799.86630.154
2.865-3.2020.2062410.16545310.16747790.970.98299.85350.184
3.202-3.6960.2131950.17940220.1842250.9740.98299.81060.209
3.696-4.5240.1781560.14734390.14836270.9820.98799.11770.183
4.524-6.3860.1911650.16626610.16728410.9830.98799.4720.221
6.386-72.7350.2851160.19715340.20316670.9360.96298.98020.256

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