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Basic information

Entry
Database: PDB / ID: 7h3p
TitleGroup deposition for crystallographic fragment screening of Coxsackievirus A16 (G-10) 2A protease -- Crystal structure of Coxsackievirus A16 (G-10) 2A protease in complex with Z100643660 (A71EV2A-x0451)
ComponentsProtease 2A
KeywordsHYDROLASE / Diamond Light Source / I03 / ASAP / Coxsackievirus A16 / crystallographic fragment screening / PanDDA / Pandda2 / XChemExplorer / viral protein
Function / homology
Function and homology information


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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity ...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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / symbiont-mediated suppression of host NF-kappaB cascade / monoatomic ion transmembrane transport / DNA replication / 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 / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein / 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) ...Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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
N,1-dimethyl-1H-indole-3-carboxamide / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLithgo, R.M. / Fairhead, M. / Koekemoer, L. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Golding, M. / Godoy, A.S. / Aschenbrenner, J.C. / Marples, P.G. ...Lithgo, R.M. / Fairhead, M. / Koekemoer, L. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Golding, M. / Godoy, A.S. / Aschenbrenner, J.C. / Marples, P.G. / Ni, X. / Thompson, W. / Tomlinson, C.W.E. / Wild, C. / Winokan, M. / Xavier, M.-A.E. / Fearon, D. / von Delft, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
CitationJournal: Biorxiv / Year: 2024
Title: Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals.
Authors: Lithgo, R.M. / Tomlinson, C.W.E. / Fairhead, M. / Winokan, M. / Thompson, W. / Wild, C. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Chandran, A.V. / Golding, M. / Koekemoer, L. / ...Authors: Lithgo, R.M. / Tomlinson, C.W.E. / Fairhead, M. / Winokan, M. / Thompson, W. / Wild, C. / Aschenbrenner, J.C. / Balcomb, B.H. / Marples, P.G. / Chandran, A.V. / Golding, M. / Koekemoer, L. / Williams, E.P. / Wang, S. / Ni, X. / MacLean, E. / Giroud, C. / Godoy, A.S. / Xavier, M.A. / Walsh, M. / Fearon, D. / von Delft, F.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0597
Polymers16,4931
Non-polymers5666
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.490, 56.580, 32.460
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protease 2A / P2A / Picornain 2A / Protein 2A


Mass: 16493.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus A16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65900, picornain 2A
#2: Chemical ChemComp-LFO / N,1-dimethyl-1H-indole-3-carboxamide


Mass: 188.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H12N2O / Source: (gene. exp.) Coxsackievirus A16 / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.05 / Details: 0.1 M MES, pH 6.05, 16 % PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.94055 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94055 Å / Relative weight: 1
ReflectionResolution: 1.5→47.3 Å / Num. obs: 24945 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.95 / Net I/σ(I): 15.6 / Num. measured all: 172445
Reflection shellResolution: 1.5→1.54 Å / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 1.262 / Num. measured all: 13149 / Num. unique obs: 1880 / CC1/2: 0.651 / Rpim(I) all: 0.509 / Rrim(I) all: 1.362 / Χ2: 0.91 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.496 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28223 1284 5.1 %RANDOM
Rwork0.22933 ---
obs0.23205 23660 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20.41 Å2
2---0.01 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 31 179 1293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0153015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141913
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.6262975
X-RAY DIFFRACTIONr_angle_other_deg1.2751.5864413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91722.019104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0811512
X-RAY DIFFRACTIONr_chiral_restr0.0540.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5332.9021580
X-RAY DIFFRACTIONr_mcbond_other1.572.831507
X-RAY DIFFRACTIONr_mcangle_it2.9734.1281398
X-RAY DIFFRACTIONr_mcangle_other2.9724.1281399
X-RAY DIFFRACTIONr_scbond_it1.5343.0411433
X-RAY DIFFRACTIONr_scbond_other1.5373.0031423
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5324.3631566
X-RAY DIFFRACTIONr_long_range_B_refined6.93834.082534
X-RAY DIFFRACTIONr_long_range_B_other6.93734.1162535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 100 -
Rwork0.34 1773 -
obs--99.84 %

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