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- PDB-6lka: Crystal Structure of EV71-3C protease with a Novel Macrocyclic Co... -

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Basic information

Entry
Database: PDB / ID: 6lka
TitleCrystal Structure of EV71-3C protease with a Novel Macrocyclic Compounds
Components3C proteinasePicornain 3C
KeywordsHYDROLASE / Enterovirus 71 / 3C Protease Inhibitor / HYDROLASE INHIBITOR / VIRUS
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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / 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 / ATP hydrolysis activity / proteolysis / 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 / 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-EGF / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.033 Å
AuthorsLi, P. / Wu, S.Q. / Xiao, T.Y.C. / Li, Y.L. / Su, Z.M. / Hao, F. / Hu, G.P. / Hu, J. / Lin, F.S. / Chen, X.S. ...Li, P. / Wu, S.Q. / Xiao, T.Y.C. / Li, Y.L. / Su, Z.M. / Hao, F. / Hu, G.P. / Hu, J. / Lin, F.S. / Chen, X.S. / Gu, Z.X. / He, H.Y. / Li, J. / Chen, S.H.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Design, synthesis, and evaluation of a novel macrocyclic anti-EV71 agent.
Authors: Li, P. / Wu, S. / Xiao, T. / Li, Y. / Su, Z. / Wei, W. / Hao, F. / Hu, G. / Lin, F. / Chen, X. / Gu, Z. / Lin, T. / He, H. / Li, J. / Chen, S.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6122
Polymers19,9761
Non-polymers6361
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.270, 64.641, 75.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 3C proteinase / Picornain 3C


Mass: 19976.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Escherichia coli (E. coli)
References: UniProt: A9XG43, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-EGF / ~{N}-[(2~{S})-1-[[(2~{S},3~{S},6~{S},7~{Z},12~{E})-4,9-bis(oxidanylidene)-6-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]-2-phenyl-1,10-dioxa-5-azacyclopentadeca-7,12-dien-3-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide


Mass: 635.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H41N5O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 9989 / % possible obs: 95.1 % / Redundancy: 3.96 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.2
Reflection shellResolution: 2.03→2.11 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 892

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
AUTOMARdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GHT

4ght


Resolution: 2.033→32.321 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 989 9.92 %
Rwork0.1955 8979 -
obs0.2021 9968 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.21 Å2 / Biso mean: 40.215 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.033→32.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 46 118 1565
Biso mean--55.2 43.23 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081483
X-RAY DIFFRACTIONf_angle_d1.0172007
X-RAY DIFFRACTIONf_chiral_restr0.059229
X-RAY DIFFRACTIONf_plane_restr0.005259
X-RAY DIFFRACTIONf_dihedral_angle_d6.731228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0333-2.14040.32971330.278119291
2.1404-2.27450.34891460.26921340100
2.2745-2.45010.33641480.251307100
2.4501-2.69650.37361440.2551134699
2.6965-3.08640.31371380.2289129297
3.0864-3.88750.24761450.1587127394
3.8875-32.3210.1681350.1492122986
Refinement TLS params.Method: refined / Origin x: 12.9537 Å / Origin y: 16.0999 Å / Origin z: -9.3203 Å
111213212223313233
T0.2782 Å2-0.0284 Å20.0755 Å2-0.2062 Å2-0.0126 Å2--0.2113 Å2
L0.9225 °20.2172 °20.0146 °2-0.8758 °20.0659 °2--0.3778 °2
S0.1073 Å °-0.0181 Å °0.0644 Å °0.4192 Å °-0.1106 Å °0.1718 Å °0.0704 Å °0.0651 Å °0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 180
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allS1 - 122

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