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- PDB-5gso: Crystal Structures of EV71 3C Protease in complex with NK-1.8k -

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Basic information

Entry
Database: PDB / ID: 5gso
TitleCrystal Structures of EV71 3C Protease in complex with NK-1.8k
Components3C protein
KeywordsHYDROLASE / EV71 3C Protease NK-1.8k
Function / homology
Function and homology information


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) / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5GI / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Major Project2014CB542800 China
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure of the Enterovirus 71 3C Protease in Complex with NK-1.8k and Indications for the Development of Antienterovirus Protease Inhibitor
Authors: Wang, Y. / Cao, L. / Zhai, Y. / Yin, Z. / Sun, Y. / Shang, L.
History
DepositionAug 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 8, 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 protein
B: 3C protein
C: 3C protein
D: 3C protein
E: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,68110
Polymers112,4585
Non-polymers2,2225
Water99155
1
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9362
Polymers22,4921
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9362
Polymers22,4921
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9362
Polymers22,4921
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9362
Polymers22,4921
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9362
Polymers22,4921
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.012, 70.691, 94.931
Angle α, β, γ (deg.)90.00, 118.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3C protein


Mass: 22491.699 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: E7E815
#2: Chemical
ChemComp-5GI / ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide


Mass: 444.456 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H25FN4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1M Tris-HCl, pH7.7, 200mM Sodium Citrate, 32% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 32158 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.4
Reflection shellResolution: 2.6→7.05 Å / Rmerge(I) obs: 0.509

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSY

3osy


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.877 / SU B: 26.192 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.745 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1720 5.1 %RANDOM
Rwork0.211 ---
obs0.215 32158 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.23 Å2
2---0.13 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 160 55 7199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9559638
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7585898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4123.71310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.171151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1211550
X-RAY DIFFRACTIONr_chiral_restr0.1190.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215323
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 109 -
Rwork0.292 2056 -
obs--86.36 %
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)
11.70360.1442-0.33360.84050.06081.32220.01160.05950.1251-0.0615-0.01540.0771-0.0235-0.10340.00380.11180.0035-0.0540.00990.01160.157-31.67114.3484103.0185
22.0185-0.2468-0.2771.0760.72352.26680.07340.12290.0479-0.10470.1386-0.056-0.17970.0861-0.2120.0649-0.01390.04970.07380.00520.109-69.39442.33195.2946
31.0465-0.03440.19921.3911-0.24541.50570.09610.06780.0436-0.1772-0.06690.03760.15050.1368-0.02920.11410.02790.01520.02350.02960.138-24.0865-27.6299115.9308
44.02980.3482-1.08732.00960.10410.9872-0.21780.6736-0.0203-0.04790.09810.14450.034-0.28090.11970.0375-0.07830.00940.2179-0.04740.0395-58.8076-30.6221120.8407
51.16290.0866-0.14761.5987-0.30531.1233-0.11-0.11480.02580.18350.00240.00160.1545-0.12850.10770.1411-0.01310.00350.1014-0.0660.0479-83.5017-30.669288.1016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 318
4X-RAY DIFFRACTION2B1 - 181
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION2B301 - 314
7X-RAY DIFFRACTION3C1 - 181
8X-RAY DIFFRACTION3C201
9X-RAY DIFFRACTION3C301 - 308
10X-RAY DIFFRACTION4D3 - 181
11X-RAY DIFFRACTION4D201
12X-RAY DIFFRACTION4D301 - 305
13X-RAY DIFFRACTION5E1 - 181
14X-RAY DIFFRACTION5E201
15X-RAY DIFFRACTION5E301 - 310

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