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- PDB-7qub: EV-A71-3Cpro in complex with inhibitor MG78 -

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Basic information

Entry
Database: PDB / ID: 7qub
TitleEV-A71-3Cpro in complex with inhibitor MG78
ComponentsProtease 3C
KeywordsVIRAL PROTEIN / Inhibitor complex / SARS-COV2
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-I70 / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsEl Kilani, H. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: Molecules / Year: 2022
Title: From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease.
Authors: Gohl, M. / Zhang, L. / El Kilani, H. / Sun, X. / Zhang, K. / Bronstrup, M. / Hilgenfeld, R.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7133
Polymers20,1391
Non-polymers5742
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.336, 122.336, 122.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11AAA-322-

HOH

21AAA-335-

HOH

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Components

#1: Protein Protease 3C / Protein 3CD / 3C protein / Picornain 3C / P3C


Mass: 20139.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8JKF9, picornain 3C
#2: Chemical ChemComp-I70 / (1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide


Mass: 550.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46N6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.84 Å3/Da / Density % sol: 67.97 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Tris-HCl pH 7.0 + 34% PEG 3350 + 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.07→43.25 Å / Num. obs: 19792 / % possible obs: 99.9 % / Redundancy: 38 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.4
Reflection shellResolution: 2.07→2.19 Å / Num. unique obs: 6525 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ghk

4ghk


Resolution: 2.07→43.25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.526 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2188 993 5.018 %
Rwork0.1915 18797 -
all0.193 --
obs-18797 99.949 %
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: 42.621 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.07→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 40 52 1505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131484
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151437
X-RAY DIFFRACTIONr_angle_refined_deg1.831.6542019
X-RAY DIFFRACTIONr_angle_other_deg1.3361.5793294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10320.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57515244
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.37151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2721511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined0.2310.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21455
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2736
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1650.26
X-RAY DIFFRACTIONr_nbd_other0.1460.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0680.24
X-RAY DIFFRACTIONr_mcbond_it3.4684.13727
X-RAY DIFFRACTIONr_mcbond_other3.464.127726
X-RAY DIFFRACTIONr_mcangle_it4.6746.183907
X-RAY DIFFRACTIONr_mcangle_other4.6756.188908
X-RAY DIFFRACTIONr_scbond_it5.7364.787757
X-RAY DIFFRACTIONr_scbond_other5.7324.786758
X-RAY DIFFRACTIONr_scangle_it7.9686.921109
X-RAY DIFFRACTIONr_scangle_other7.9646.9191110
X-RAY DIFFRACTIONr_lrange_it9.49749.3661535
X-RAY DIFFRACTIONr_lrange_other9.48349.3041531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.120.313660.3171350X-RAY DIFFRACTION99.9294
2.12-2.1780.364760.3091301X-RAY DIFFRACTION100
2.178-2.2410.308680.2841293X-RAY DIFFRACTION99.9266
2.241-2.310.241640.2551256X-RAY DIFFRACTION100
2.31-2.3860.248630.2391213X-RAY DIFFRACTION100
2.386-2.470.267560.2481182X-RAY DIFFRACTION100
2.47-2.5630.255600.2331138X-RAY DIFFRACTION100
2.563-2.6670.316540.2391113X-RAY DIFFRACTION100
2.667-2.7860.255410.2351073X-RAY DIFFRACTION100
2.786-2.9220.26570.2121011X-RAY DIFFRACTION100
2.922-3.080.198480.2970X-RAY DIFFRACTION100
3.08-3.2670.201660.183905X-RAY DIFFRACTION100
3.267-3.4920.216420.174872X-RAY DIFFRACTION100
3.492-3.7710.168410.164818X-RAY DIFFRACTION100
3.771-4.1310.173500.159749X-RAY DIFFRACTION100
4.131-4.6180.165420.134686X-RAY DIFFRACTION100
4.618-5.3310.212360.151621X-RAY DIFFRACTION100
5.331-6.5260.266260.177541X-RAY DIFFRACTION100
6.526-9.2160.184230.147433X-RAY DIFFRACTION99.7812
9.216-43.250.213150.206275X-RAY DIFFRACTION97.6431

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