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- PDB-5iyt: Complex structure of EV-B93 main protease 3C with N-Ethyl 4-((1-c... -

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Basic information

Entry
Database: PDB / ID: 5iyt
TitleComplex structure of EV-B93 main protease 3C with N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-2Z-butenamide
ComponentsEV-B93 main protease 3C
KeywordsHYDROLASE / 3C main protease / Enterovirus B93 / covalent inhibitor
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / nucleoside-triphosphate phosphatase / channel activity ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / nucleoside-triphosphate phosphatase / channel activity / 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 VP4 superfamily / 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 VP4 superfamily / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-NZN / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKaczmarska, Z. / Becker, D. / Rademann, J. / Coll, M.
CitationJournal: Nat Commun / Year: 2016
Title: Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments.
Authors: Becker, D. / Kaczmarska, Z. / Arkona, C. / Schulz, R. / Tauber, C. / Wolber, G. / Hilgenfeld, R. / Coll, M. / Rademann, J.
History
DepositionMar 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EV-B93 main protease 3C
B: EV-B93 main protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1133
Polymers42,7912
Non-polymers3221
Water3,279182
1
A: EV-B93 main protease 3C


Theoretical massNumber of molelcules
Total (without water)21,3961
Polymers21,3961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EV-B93 main protease 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7182
Polymers21,3961
Non-polymers3221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.460, 52.330, 62.270
Angle α, β, γ (deg.)90.00, 103.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EV-B93 main protease 3C


Mass: 21395.512 Da / Num. of mol.: 2 / Mutation: M137V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echovirus 1 (strain Human/Egypt/Farouk/1951)
Plasmid: pDEST / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O91734, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C
#2: Chemical ChemComp-NZN / N-Ethyl 4-((1-cycloheptyl-1,2-dihydropyrazol-3-one-5-yl)-amino)-4-oxo-butanamide


Mass: 322.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG3350, ammonium acetate, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 36576 / % possible obs: 97.1 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.05
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.14 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q3X

3q3x


Resolution: 1.73→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.555 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21727 1794 4.9 %RANDOM
Rwork0.18741 ---
obs0.18889 34781 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20.14 Å2
2---0.72 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.73→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 23 182 3037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192963
X-RAY DIFFRACTIONr_bond_other_d0.0020.022875
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.974009
X-RAY DIFFRACTIONr_angle_other_deg0.86136600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26623.75136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35915506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5791520
X-RAY DIFFRACTIONr_chiral_restr0.0710.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
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_it1.2042.7211466
X-RAY DIFFRACTIONr_mcbond_other1.1982.721465
X-RAY DIFFRACTIONr_mcangle_it2.0624.0741832
X-RAY DIFFRACTIONr_mcangle_other2.0614.0751833
X-RAY DIFFRACTIONr_scbond_it1.4593.0231497
X-RAY DIFFRACTIONr_scbond_other1.4583.0251498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4934.4372172
X-RAY DIFFRACTIONr_long_range_B_refined5.06922.7073244
X-RAY DIFFRACTIONr_long_range_B_other4.94622.53201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 142 -
Rwork0.282 2486 -
obs--96.26 %

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