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- PDB-9na0: Main protease of HKU8 in complex with AVI8122 -

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Basic information

Entry
Database: PDB / ID: 9na0
TitleMain protease of HKU8 in complex with AVI8122
Componentsmain protease
KeywordsVIRAL PROTEIN / main protease / Nsp5 / HKU8 / inhibitor
Function / homology: / :
Function and homology information
Biological speciesMiniopterus bat coronavirus HKU8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, P. / Lu, J. / Lemieux, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Identification of Inhibitors Broadly Against Main Proteases of coronavirus
Authors: Chen, P. / Lu, J. / Lemieux, M.J.
History
DepositionFeb 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3942
Polymers32,9191
Non-polymers4751
Water4,161231
1
A: main protease
hetero molecules

A: main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7884
Polymers65,8392
Non-polymers9492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2480 Å2
ΔGint-15 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 57.987, 106.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21A-692-

HOH

31A-699-

HOH

41A-704-

HOH

51A-729-

HOH

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Components

#1: Protein main protease / Nsp5


Mass: 32919.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Miniopterus bat coronavirus HKU8 / Gene: orf1ab, 6610_gp1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6B9KKB5
#2: Chemical ChemComp-A1BWH / N-[(2S)-3-cyclopropyl-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}amino)-1-oxopropan-2-yl]-7-fluoro-1H-indole-2-carboxamide


Mass: 474.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31FN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Citrate pH 5.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→43.26 Å / Num. obs: 27810 / % possible obs: 99.64 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1622 / Net I/σ(I): 11.28
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 2713 / CC1/2: 0.542

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.26 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1358 4.88 %
Rwork0.1974 --
obs0.1979 27807 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 34 231 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072387
X-RAY DIFFRACTIONf_angle_d0.9323240
X-RAY DIFFRACTIONf_dihedral_angle_d15.539840
X-RAY DIFFRACTIONf_chiral_restr0.055358
X-RAY DIFFRACTIONf_plane_restr0.01420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.34441210.33962546X-RAY DIFFRACTION98
1.86-1.940.31961130.28452644X-RAY DIFFRACTION100
1.94-2.030.28171230.24922625X-RAY DIFFRACTION100
2.03-2.130.25451320.23182627X-RAY DIFFRACTION100
2.13-2.270.27331530.22732589X-RAY DIFFRACTION100
2.27-2.440.23961510.22042603X-RAY DIFFRACTION100
2.44-2.690.23021270.21872649X-RAY DIFFRACTION99
2.69-3.080.21071340.21132671X-RAY DIFFRACTION100
3.08-3.870.17431420.17192699X-RAY DIFFRACTION100
3.87-43.260.16421620.15722796X-RAY DIFFRACTION99

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