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- PDB-3q3y: Complex structure of HEVB EV93 main protease 3C with Compound 1 (... -

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Basic information

Entry
Database: PDB / ID: 3q3y
TitleComplex structure of HEVB EV93 main protease 3C with Compound 1 (AG7404)
ComponentsHEVB EV93 3C protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine trypsin-like protease / 3C cysteine protease (picornain 3C) / antiviral Compound 1 (AG7404) / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...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 / 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 / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / 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) / 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 / 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
AMMONIUM ION / HYDROGENPHOSPHATE ION / Chem-XNV / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å
AuthorsCostenaro, L. / Kaczmarska, Z. / Arnan, C. / Sola, M. / Coutard, B. / Norder, H. / Canard, B. / Coll, M.
CitationJournal: J.Virol. / Year: 2011
Title: Structural Basis for Antiviral Inhibition of the Main Protease, 3C, from Human Enterovirus 93.
Authors: Costenaro, L. / Kaczmarska, Z. / Arnan, C. / Janowski, R. / Coutard, B. / Sola, M. / Gorbalenya, A.E. / Norder, H. / Canard, B. / Coll, M.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEVB EV93 3C protease
B: HEVB EV93 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,66317
Polymers42,7912
Non-polymers1,87215
Water9,782543
1
A: HEVB EV93 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,39710
Polymers21,3961
Non-polymers1,0029
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEVB EV93 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2657
Polymers21,3961
Non-polymers8706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.040, 64.450, 68.740
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HEVB EV93 3C protease


Mass: 21395.512 Da / Num. of mol.: 2 / Mutation: M139V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus B / Gene: 3C / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5DSM6, picornain 3C

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Non-polymers , 5 types, 558 molecules

#2: Chemical ChemComp-XNV / ethyl (4R)-4-({(2S)-2-[3-{[(5-methyl-1,2-oxazol-3-yl)carbonyl]amino}-2-oxopyridin-1(2H)-yl]pent-4-ynoyl}amino)-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate / AG7404, bound form


Mass: 525.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H31N5O7
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO4P
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THIS MAY BE A NATURAL VARIANT.

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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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 1.8 M (NH4)2HPO4, 0.1 M Tris, cryo + 13.4% ethylene glycol, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2010 / Details: mirrors
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.32→39.036 Å / Num. all: 79978 / Num. obs: 79978 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.2
Reflection shellResolution: 1.32→1.3672 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 5.2 / Num. unique all: 79978 / Rsym value: 0.085 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.3 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.37 Å
Translation2.5 Å34.37 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q3X

3q3x


Resolution: 1.32→39.036 Å / Occupancy max: 1 / Occupancy min: 0.11 / SU ML: 0.15 / Isotropic thermal model: anisotropic (no H, No water) / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
Details: hydrogens added in the riding positions, occupancies refined
RfactorNum. reflection% reflectionSelection details
Rfree0.1701 4013 5.02 %random
Rwork0.1252 ---
obs0.1275 79928 99.95 %-
all-79928 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.768 Å2 / ksol: 0.457 e/Å3
Displacement parametersBiso max: 104.01 Å2 / Biso mean: 17.8614 Å2 / Biso min: 3.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.2663 Å2-0 Å20.9489 Å2
2---0.8874 Å20 Å2
3----0.3789 Å2
Refinement stepCycle: LAST / Resolution: 1.32→39.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 125 543 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123618
X-RAY DIFFRACTIONf_angle_d1.6014942
X-RAY DIFFRACTIONf_chiral_restr0.089519
X-RAY DIFFRACTIONf_plane_restr0.015657
X-RAY DIFFRACTIONf_dihedral_angle_d16.1041515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.32-1.36720.25073960.206975777973
1.3672-1.42190.25674050.184975707975
1.4219-1.48660.21133870.143375257912
1.4866-1.5650.19393750.124976398014
1.565-1.66310.16644020.112775477949
1.6631-1.79150.15853750.109175887963
1.7915-1.97180.16513960.114276208016
1.9718-2.25710.15084460.110275327978
2.2571-2.84350.1633850.117676528037
2.8435-39.05320.15324460.12476658111

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