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- PDB-5j4y: The crystal structure of N-(4-(2-(thiazolo[5,4-c]pyridin-2-yl)phe... -

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Basic information

Entry
Database: PDB / ID: 5j4y
TitleThe crystal structure of N-(4-(2-(thiazolo[5,4-c]pyridin-2-yl)phenoxy)phenyl)acetamide bound to JCV Helicase
ComponentsLarge T antigenLarge tumor antigen
KeywordsHYDROLASE/INHIBITOR / Helicase / hexamer / Zn / ATP / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / metal ion binding
Similarity search - Function
Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6JG / Large T antigen
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.59 Å
AuthorsTer Haar, E.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Fragment-Based Discovery of Dual JC Virus and BK Virus Helicase Inhibitors.
Authors: Bonafoux, D. / Nanthakumar, S. / Bandarage, U.K. / Memmott, C. / Lowe, D. / Aronov, A.M. / Bhisetti, G.R. / Bonanno, K.C. / Coll, J. / Leeman, J. / Lepre, C.A. / Lu, F. / Perola, E. / ...Authors: Bonafoux, D. / Nanthakumar, S. / Bandarage, U.K. / Memmott, C. / Lowe, D. / Aronov, A.M. / Bhisetti, G.R. / Bonanno, K.C. / Coll, J. / Leeman, J. / Lepre, C.A. / Lu, F. / Perola, E. / Rijnbrand, R. / Taylor, W.P. / Wilson, D. / Zhou, Y. / Zwahlen, J. / Ter Haar, E.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2036
Polymers42,3891
Non-polymers8145
Water1,62190
1
A: Large T antigen
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)259,21936
Polymers254,3346
Non-polymers4,88530
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area21800 Å2
ΔGint-249 kcal/mol
Surface area89480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.250, 109.250, 66.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Large T antigen / Large tumor antigen / LT-AG


Mass: 42388.984 Da / Num. of mol.: 1 / Fragment: UNP residues 261-628
Mutation: E280A, D295N, N299A, Q301A, Q302A, K304A, K305A, E307A, K308A, K309A, I354L, D408E, R624A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Production host: Escherichia coli (E. coli)
References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 95 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-6JG / N-{4-[2-([1,3]thiazolo[5,4-c]pyridin-2-yl)phenoxy]phenyl}acetamide


Mass: 361.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15N3O2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25-30% Peg400, 0.1 M LiSO4, 0.1M HEPES (pH 7.0), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→54.62 Å / Num. obs: 14072 / % possible obs: 98.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 75.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.59-2.735.70.771199.5
8.19-54.625.50.016196.1

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 2.59→54.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.545 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.532 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.238 699 4.98 %RANDOM
Rwork0.17 ---
obs0.173 14047 98.4 %-
Displacement parametersBiso max: 167.76 Å2 / Biso mean: 75.12 Å2 / Biso min: 34.79 Å2
Baniso -1Baniso -2Baniso -3
1-2.9482 Å20 Å20 Å2
2--2.9482 Å20 Å2
3----5.8965 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.59→54.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 62 90 3020
Biso mean--87.28 69.03 -
Num. residues----363
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1043SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes455HARMONIC5
X-RAY DIFFRACTIONt_it2991HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3499SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2991HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4061HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion20.25
LS refinement shellResolution: 2.59→2.8 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.291 141 4.87 %
Rwork0.206 2756 -
all-2897 -
obs--99.11 %
Refinement TLS params.

T11: -0.1519 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.58420.5897-0.32484.48581.4353.72960.04890.1170.1227-0.0750.18640.69930.0034-0.4745-0.23540.0110.0275-0.04690.1655-0.0087-23.59227.7415-12.391
24.5823-0.0367-0.38792.3244-0.41221.43330.3981-0.1336-0.07710.0372-0.2393-0.1897-0.11180.1271-0.1588-0.03280.0543-0.19140.0685-0.0754-31.306119.21115.1464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|701 - A|701 A|266 - A|356 }A701
2X-RAY DIFFRACTION1{ A|701 - A|701 A|266 - A|356 }A266 - 356
3X-RAY DIFFRACTION2{ A|357 - A|512 A|518 - A|628 }A357 - 512
4X-RAY DIFFRACTION2{ A|357 - A|512 A|518 - A|628 }A518 - 628

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