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- PDB-7da6: Enterovirus 71 2A Protease mutant- C110A in complex with peptide ... -

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Basic information

Entry
Database: PDB / ID: 7da6
TitleEnterovirus 71 2A Protease mutant- C110A in complex with peptide inhibitor
Components
  • PHE-ARG-GLY-LYS
  • PolyproteinProteolysis
KeywordsVIRAL PROTEIN / 2A protease
Function / homology
Function and homology information


virion component => GO:0044423 / viral process / peptidase activity / host cell cytoplasm / cytoplasm
Similarity search - Function
Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHuman enterovirus 71
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsYang, W.Z. / Yuan, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Bio Med Chem Au / Year: 2022
Title: Efficient Strategy to Design Protease Inhibitors: Application to Enterovirus 71 2A Protease.
Authors: Chen, T. / Grauffel, C. / Yang, W.Z. / Chen, Y.P. / Yuan, H.S. / Lim, C.
History
DepositionOct 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_audit_support / pdbx_contact_author / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_overall_phase_error / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_chi_squared / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_number_measured_all / _software.classification / _software.name / _software.version / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Description: Model orientation/position
Details: correct the orientation on N-terminus of peptide inhibitor
Provider: author / Type: Coordinate replacement
Revision 2.1Jun 29, 2022Group: Database references / Category: citation / citation_author
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.title / _citation.year
Revision 2.2Nov 29, 2023Group: 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
A: Polyprotein
C: PHE-ARG-GLY-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7723
Polymers15,7072
Non-polymers651
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.476, 44.407, 51.369
Angle α, β, γ (deg.)90.000, 111.570, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polyprotein / Proteolysis


Mass: 15197.961 Da / Num. of mol.: 1 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: E5L197
#2: Protein/peptide PHE-ARG-GLY-LYS


Mass: 508.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.5), 20% 2-propanol, and 10% polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 9107 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.78 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.075 / Χ2: 1.418 / Net I/σ(I): 9.8 / Num. measured all: 32175
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.50.3124450.8820.1920.3670.7398.7
2.24-2.283.60.3334460.8670.20.3890.8699.1
2.28-2.323.60.2534580.950.1530.2970.84299.1
2.32-2.373.60.2554360.9170.1550.30.95999.3
2.37-2.423.60.2324710.9440.1420.2720.94999.6
2.42-2.483.60.1954430.9580.1190.2290.97899.6
2.48-2.543.50.1874590.9630.1140.2190.98999.6
2.54-2.613.60.1784550.9640.1090.2091.13899.3
2.61-2.683.60.154540.9730.0910.1761.19998.7
2.68-2.773.60.1394500.9710.0850.1631.42899.6
2.77-2.873.50.1264550.9740.0770.1481.7199.3
2.87-2.993.50.0994630.9860.0610.1171.61199.6
2.99-3.123.50.094370.9840.0560.1061.80598.6
3.12-3.293.50.0744660.990.0460.0881.66199.4
3.29-3.493.50.064530.9940.0380.0711.73598.5
3.49-3.763.40.0484600.9950.0310.0581.79598.5
3.76-4.143.40.0454520.9960.0290.0532.11996.8
4.14-4.733.60.0414620.9960.0250.0481.97698.9
4.73-5.963.50.0464650.9910.0290.0541.93499.1
5.96-303.40.0434770.9950.0270.052.04796.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4-1496refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fvb

4fvb


Resolution: 2.2→22.754 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 910 10 %
Rwork0.1865 8193 -
obs0.1923 9103 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.99 Å2 / Biso mean: 41.96 Å2 / Biso min: 18.24 Å2
Refinement stepCycle: final / Resolution: 2.2→22.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 1 48 1152
Biso mean--43.83 47.66 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111136
X-RAY DIFFRACTIONf_angle_d1.2241541
X-RAY DIFFRACTIONf_chiral_restr0.054164
X-RAY DIFFRACTIONf_plane_restr0.006201
X-RAY DIFFRACTIONf_dihedral_angle_d13.217399
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.31370.31851230.2195110895
2.3137-2.45850.30931310.21921176100
2.4585-2.64810.29651290.2249116699
2.6481-2.91410.2781310.2202117699
2.9141-3.33470.27881320.1987118099
3.3347-4.1970.21281290.1672117298
4.197-22.750.20221350.1655121598

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