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- PDB-3fci: Complex of UNG2 and a fragment-based designed inhibitor -

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Basic information

Entry
Database: PDB / ID: 3fci
TitleComplex of UNG2 and a fragment-based designed inhibitor
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA REPAIR / URACIL / URACIL DNA GLYCOSYLASE / Alternative splicing / Disease mutation / DNA damage / Glycosidase / Host-virus interaction / Mitochondrion / Nucleus / Phosphoprotein / Transit peptide
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3FI / THIOCYANATE ION / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.27 Å
AuthorsBianchet, M.A. / Chung, S. / Parker, J.B. / Amzel, L.M. / Stivers, J.T.
Citation
Journal: Nat.Chem.Biol. / Year: 2009
Title: Impact of linker strain and flexibility in the design of a fragment-based inhibitor
Authors: Chung, S. / Parker, J.B. / Bianchet, M. / Amzel, L.M. / Stivers, J.T.
#1: Journal: J.Am.Chem.Soc. / Year: 2005
Title: Uracil-directed ligand tethering: an efficient strategy for uracil DNA glycosylase (UNG) inhibitor development
Authors: Jiang, T.L. / Krosky, D.J. / Seiple, L. / Stivers, J.T.
#2: Journal: Nucleic Acids Res. / Year: 2006
Title: Mimicking damaged DNA with a small molecule inhibitor of human UNG2.
Authors: Krosky, D.J. / Bianchet, M.A. / Seiple, L. / Chung, S. / Amzel, L.M. / Stivers, J.T.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0305
Polymers25,5441
Non-polymers4854
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.014, 68.476, 69.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 25544.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNG, DGU, UNG1, UNG15 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P13051, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-3FI / 3-{(E)-[(3-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}propoxy)imino]methyl}benzoic acid


Mass: 346.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 microliter of the solution: 0.001 M UNG2 0.05 M TRIS-OAC pH 7.0 0.15 M NACL 0.001 M DTT 0.005 M inhibitor, was mixed with equal amount of the solution containing 0.16 M KSCN AND 22% PEG ...Details: 1 microliter of the solution: 0.001 M UNG2 0.05 M TRIS-OAC pH 7.0 0.15 M NACL 0.001 M DTT 0.005 M inhibitor, was mixed with equal amount of the solution containing 0.16 M KSCN AND 22% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. obs: 45064 / % possible obs: 81 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Χ2: 3.026
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.26-1.311.30.2759001.07916.5
1.31-1.361.90.19823580.97943
1.36-1.422.50.16536361.23766.1
1.42-1.493.30.13447171.70285.9
1.49-1.594.80.11953912.14397.5
1.59-1.716.70.10255222.586100
1.71-1.886.80.07955423.032100
1.88-2.156.80.06355823.501100
2.15-2.716.80.05256353.429100
2.71-506.20.05157814.12298.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.27→27.08 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.771 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2283 5.1 %RANDOM
Rwork0.174 ---
obs0.176 45025 80.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.26 Å2 / Biso mean: 18.334 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.27→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 32 495 2356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221923
X-RAY DIFFRACTIONr_angle_refined_deg1.4412.0572606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28923.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71815310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.581158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021504
X-RAY DIFFRACTIONr_nbd_refined0.2150.21003
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2380
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.274
X-RAY DIFFRACTIONr_mcbond_it0.6511.51124
X-RAY DIFFRACTIONr_mcangle_it1.221818
X-RAY DIFFRACTIONr_scbond_it1.8853843
X-RAY DIFFRACTIONr_scangle_it3.0324.5788
LS refinement shellResolution: 1.27→1.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 22 -
Rwork0.384 465 -
all-487 -
obs--12.07 %

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