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- PDB-9owc: Human WRN helicase in complex with allosteric ligand Compound 7 -

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Basic information

Entry
Database: PDB / ID: 9owc
TitleHuman WRN helicase in complex with allosteric ligand Compound 7
ComponentsBifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
KeywordsHYDROLASE / WRN / Werner / helicase
Function / homology
Function and homology information


positive regulation of hydrolase activity / 3'-flap-structured DNA binding / positive regulation of strand invasion / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / t-circle formation ...positive regulation of hydrolase activity / 3'-flap-structured DNA binding / positive regulation of strand invasion / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / t-circle formation / telomeric D-loop disassembly / DNA geometric change / Y-form DNA binding / four-way junction helicase activity / G-quadruplex DNA binding / bubble DNA binding / MutLalpha complex binding / Impaired BRCA2 binding to PALB2 / protein localization to nucleolus / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / response to UV-C / exonuclease activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / DNA synthesis involved in DNA repair / Impaired BRCA2 binding to RAD51 / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / mismatch repair / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / 3'-5' exonuclease activity / telomere maintenance / DNA helicase activity / cellular response to starvation / replication fork / determination of adult lifespan / cellular response to gamma radiation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / base-excision repair / HDR through Homologous Recombination (HRR) / cellular senescence / double-strand break repair / manganese ion binding / chromosome / Processing of DNA double-strand break ends / response to oxidative stress / Regulation of TP53 Activity through Phosphorylation / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / nuclear speck / DNA damage response / centrosome / protein-containing complex binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPalte, R.L. / Koglin, M. / Maskos, K. / Tauchert, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Slas Discov / Year: 2025
Title: High-throughput evaluation of novel WRN inhibitors.
Authors: Xu, H. / Palte, R.L. / Rickard, M.M. / Kwon, S.W. / Chai, X. / Yuan, J. / Bassett, J. / Moran, J. / Koglin, M. / Musisi, I. / Zhang, M. / Maskos, K. / Tauchert, M.J. / Cheng, Y.S. / Wang, Z. ...Authors: Xu, H. / Palte, R.L. / Rickard, M.M. / Kwon, S.W. / Chai, X. / Yuan, J. / Bassett, J. / Moran, J. / Koglin, M. / Musisi, I. / Zhang, M. / Maskos, K. / Tauchert, M.J. / Cheng, Y.S. / Wang, Z. / Yang, Y. / Banerjee, A. / Chen, J.L. / Bharathan, I. / Rico, L. / Logan, K. / Mansueto, M.S. / Shumway, S. / Methot, J.L. / Bauer, R.J.
History
DepositionJun 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,82212
Polymers50,4811
Non-polymers1,34111
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint28 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.780, 58.358, 132.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN / DNA helicase / RecQ-like type 3 / RecQ protein-like 2 / Werner syndrome protein


Mass: 50480.906 Da / Num. of mol.: 1 / Fragment: UNP residues 500-942
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Gene: WRN, RECQ3, RECQL2 / Production host: Homo sapiens (human)
References: UniProt: Q14191, Hydrolases; Acting on ester bonds, DNA 3'-5' helicase

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Non-polymers , 5 types, 294 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1CEY / N-[2-chloro-4-(trifluoromethyl)phenyl]-2-[(5S,9R)-1'-(3-hydroxypyridine-2-carbonyl)-5-methyl-2-(morpholin-4-yl)-8-oxo-5,8-dihydrospiro[cyclopenta[d][1,2,4]triazolo[1,5-a]pyrimidine-7,4'-piperidin]-4(6H)-yl]acetamide


Mass: 701.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H32ClF3N8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.668→66.083 Å / Num. obs: 52706 / % possible obs: 99.7 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.3
Reflection shellResolution: 1.668→1.697 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2579 / CC1/2: 0.53 / % possible all: 99.1

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→66.08 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.106 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20624 5395 10.2 %RANDOM
Rwork0.15623 ---
obs0.16138 47310 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.2 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.67→66.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 86 283 3810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133608
X-RAY DIFFRACTIONr_bond_other_d0.0090.0173428
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.6694890
X-RAY DIFFRACTIONr_angle_other_deg1.2721.5877891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00921.967183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96115.095634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8331524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024075
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02822
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_it2.1513.2121758
X-RAY DIFFRACTIONr_mcbond_other2.1383.2111757
X-RAY DIFFRACTIONr_mcangle_it2.8094.8252204
X-RAY DIFFRACTIONr_mcangle_other2.8094.8262205
X-RAY DIFFRACTIONr_scbond_it2.383.5361850
X-RAY DIFFRACTIONr_scbond_other2.3793.5371851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0255.1462674
X-RAY DIFFRACTIONr_long_range_B_refined4.12538.5333999
X-RAY DIFFRACTIONr_long_range_B_other3.99638.223953
X-RAY DIFFRACTIONr_rigid_bond_restr2.37837036
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.711 Å
RfactorNum. reflection% reflection
Rfree0.309 399 -
Rwork0.265 3435 -
obs--99.1 %

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