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- PDB-7dnc: Crystal structure of EV71 3C proteinase in complex with a novel i... -

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Basic information

Entry
Database: PDB / ID: 7dnc
TitleCrystal structure of EV71 3C proteinase in complex with a novel inhibitor
Components3C protease
KeywordsHYDROLASE / 3Cpro / inhibitor / complex
Function / homology
Function and homology information


RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-FHR / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.17 Å
AuthorsXie, H. / Su, H.X. / Li, M.J. / Xu, Y.C.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Design, Synthesis, and Biological Evaluation of Peptidomimetic Aldehydes as Broad-Spectrum Inhibitors against Enterovirus and SARS-CoV-2.
Authors: Dai, W. / Jochmans, D. / Xie, H. / Yang, H. / Li, J. / Su, H. / Chang, D. / Wang, J. / Peng, J. / Zhu, L. / Nian, Y. / Hilgenfeld, R. / Jiang, H. / Chen, K. / Zhang, L. / Xu, Y. / Neyts, J. / Liu, H.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5872
Polymers20,1341
Non-polymers4531
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8440 Å2
Unit cell
Length a, b, c (Å)95.034, 95.034, 34.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

21A-405-

HOH

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Components

#1: Protein 3C protease / Protein 3B / Viral protein genome-linked


Mass: 20134.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8YLW0
#2: Chemical ChemComp-FHR / ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide


Type: peptide-like / Mass: 452.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES monohydrate (pH 6.0), 20% 2-propanol, 20% polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.17→31.48 Å / Num. obs: 59502 / % possible obs: 99.3 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.009 / Rrim(I) all: 0.04 / Net I/σ(I): 32.8 / Num. measured all: 1128639 / Scaling rejects: 72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.17-1.2314.50.87412207384280.860.2340.9062.796.9
3.69-31.4817.80.02235640200210.0050.023118.199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.45 Å31.48 Å
Translation4.45 Å31.48 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GHT

4ght


Resolution: 1.17→20.58 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1866 3041 5.11 %
Rwork0.1799 56429 -
obs0.1802 59470 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.54 Å2 / Biso mean: 20.0193 Å2 / Biso min: 10.75 Å2
Refinement stepCycle: final / Resolution: 1.17→20.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 33 138 1543
Biso mean--13.61 29.32 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.17-1.190.29721450.24692438258396
1.19-1.210.24181540.23922461261597
1.21-1.230.27391380.23082504264298
1.23-1.250.21011330.222125482681100
1.25-1.270.21151180.22342532265098
1.27-1.30.22291410.217125772718100
1.3-1.330.24951220.20682535265798
1.33-1.360.19661170.196925882705100
1.36-1.390.19721400.19452546268699
1.39-1.430.21461380.19422552269099
1.43-1.470.17441300.18825852715100
1.47-1.520.18341470.182825592706100
1.52-1.570.20181660.183625282694100
1.57-1.640.18871180.176226172735100
1.64-1.710.20281220.179225992721100
1.71-1.80.20611370.179825882725100
1.8-1.910.17681540.17525742728100
1.91-2.060.16291400.172525842724100
2.06-2.270.16631380.169226052743100
2.27-2.590.19431400.17726102750100
2.6-3.270.18781590.183826052764100
3.27-20.580.17051440.166726942838100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.41261.03234.57916.07910.38958.66450.151-0.3126-0.12570.5490.17110.29770.4764-0.1308-0.26110.29020.02940.05620.13990.04050.1443-27.119415.48379.8608
22.377-0.3484-0.3753.76150.49123.8735-0.02610.1622-0.0262-0.10970.01990.1780.2842-0.15690.01840.1137-0.0121-0.00770.12010.01020.1258-28.999118.5765-5.9361
33.50930.6257-0.10693.8020.29923.88130.07490.1517-0.1393-0.3116-0.05680.31910.0276-0.1983-0.01330.12850.0197-0.02250.12630.00780.1536-31.749121.7063-9.5466
46.44090.95090.7267.62030.88061.54670.05260.19940.2043-0.05290.03980.6947-0.0196-0.181-0.08160.15330.0163-0.01740.17180.01390.1251-36.413725.3504-10.8581
52.91710.17730.24142.7762-0.20861.89170.0087-0.09540.33120.0072-0.0453-0.0751-0.11110.03160.03580.11570.0230.00820.09390.00040.1417-24.579733.682-8.3118
66.08752.64438.0582.47853.17462.04620.3983-0.8714-0.11140.3533-0.25340.33040.2238-0.8981-0.14860.2199-0.0840.05080.36210.00910.2014-36.382824.39953.8969
78.00691.15650.23744.6343-1.15714.56020.2053-0.55880.85070.4587-0.1121-0.1274-0.06190.0974-0.08780.2283-0.05880.02730.1627-0.06420.1239-17.558530.85037.4099
85.24261.66090.10484.93520.66563.5157-0.17580.2595-0.293-0.08720.08250.00140.2670.00590.09560.1323-0.00850.01080.09740.010.1222-22.108512.3297-1.5179
93.29064.0815-1.75146.7792-2.23181.18660.1909-0.251-0.33140.2205-0.3116-0.42940.04670.19990.11550.1495-0.0038-0.03260.1540.0130.1459-12.377321.23722.4875
102.7522-0.2436-2.13353.90721.29993.42970.1470.25980.1851-0.2954-0.06620.0133-0.3647-0.1167-0.09620.1205-0.0073-0.00160.13370.01960.1571-12.40130.8969-8.2007
112.01830.47182.86031.1016-0.23732.872-0.00740.1429-0.32560.05740.027-0.1420.20980.21040.00610.16310.01470.01470.13380.00540.1735-13.862116.423-4.5032
123.3496-0.2551-1.16781.87060.4172.67180.1284-0.19510.18680.1315-0.0463-0.0535-0.11380.0103-0.0650.1219-0.0222-0.00010.0934-0.00380.1129-18.75726.52180.0587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 13 )A3 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 31 )A14 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 51 )A32 - 51
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 61 )A52 - 61
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 77 )A62 - 77
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 89 )A78 - 89
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 99 )A90 - 99
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 111 )A100 - 111
9X-RAY DIFFRACTION9chain 'A' and (resid 112 through 123 )A112 - 123
10X-RAY DIFFRACTION10chain 'A' and (resid 124 through 138 )A124 - 138
11X-RAY DIFFRACTION11chain 'A' and (resid 139 through 149 )A139 - 149
12X-RAY DIFFRACTION12chain 'A' and (resid 150 through 181 )A150 - 181

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