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- PDB-8j3t: Complex structure of human cytomegalovirus protease and a non-cov... -

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Basic information

Entry
Database: PDB / ID: 8j3t
TitleComplex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand
ComponentsAssemblin
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


assemblin / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21)
Similarity search - Domain/homology
Chem-T1F / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYoshida, S. / Sako, Y. / Nikaido, E. / Ueda, T. / Kozono, I. / Ichihashi, Y. / Nakahashi, A. / Onishi, M. / Yamatsu, Y. / Kato, T. ...Yoshida, S. / Sako, Y. / Nikaido, E. / Ueda, T. / Kozono, I. / Ichihashi, Y. / Nakahashi, A. / Onishi, M. / Yamatsu, Y. / Kato, T. / Nishikawa, J. / Tachibana, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Authors: Yoshida, S. / Sako, Y. / Nikaido, E. / Ueda, T. / Kozono, I. / Ichihashi, Y. / Nakahashi, A. / Onishi, M. / Yamatsu, Y. / Kato, T. / Nishikawa, J. / Tachibana, Y.
History
DepositionApr 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Assemblin
B: Assemblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6374
Polymers58,2612
Non-polymers1,3762
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-19 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.364, 76.364, 215.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Assemblin / / Protease


Mass: 29130.686 Da / Num. of mol.: 2 / Mutation: A143Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Gene: UL80 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2TMR2, assemblin
#2: Chemical ChemComp-T1F / (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide


Mass: 687.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H45N7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M MES pH 5.5, 0.6 M NaCl, 0.097 M ammonium acetate, 0.005 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→71.96 Å / Num. obs: 16515 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Net I/σ(I): 15.2
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2345 / CC1/2: 0.959

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→71.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.871 / SU B: 19.829 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R: 1.01 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30945 743 5 %RANDOM
Rwork0.22426 ---
obs0.22864 14107 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.361 Å2
Baniso -1Baniso -2Baniso -3
1-5.29 Å2-0 Å2-0 Å2
2--5.29 Å2-0 Å2
3----10.58 Å2
Refinement stepCycle: 1 / Resolution: 2.9→71.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 102 1 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193261
X-RAY DIFFRACTIONr_bond_other_d0.0020.022946
X-RAY DIFFRACTIONr_angle_refined_deg1.7552.0094457
X-RAY DIFFRACTIONr_angle_other_deg0.8936749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55122.366131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.31215447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
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_it5.6327.9321649
X-RAY DIFFRACTIONr_mcbond_other5.637.9291646
X-RAY DIFFRACTIONr_mcangle_it8.60911.862045
X-RAY DIFFRACTIONr_mcangle_other8.60611.862045
X-RAY DIFFRACTIONr_scbond_it5.2918.1451612
X-RAY DIFFRACTIONr_scbond_other5.298.1461613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1912.1022413
X-RAY DIFFRACTIONr_long_range_B_refined11.93193.9853691
X-RAY DIFFRACTIONr_long_range_B_other11.92993.9933692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 47 -
Rwork0.376 1010 -
obs--100 %

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