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- PDB-6w7j: Structure of Tdp1 catalytic domain in complex with inhibitor XZ635p -

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Basic information

Entry
Database: PDB / ID: 6w7j
TitleStructure of Tdp1 catalytic domain in complex with inhibitor XZ635p
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsHYDROLASE/HYDROLASE Inhibitor / phosphodiesterase / inhibitor / cancer drug target / DNA BINDING PROTEIN / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair ...3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tyrosyl-DNA phosphodiesterase I / Tyrosyl-DNA phosphodiesterase
Similarity search - Domain/homology
Chem-TGM / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S.
CitationJournal: To Be Published
Title: Tdp1 catalytic domain
Authors: Lountos, G.T. / Waugh, D.S.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosyl-DNA phosphodiesterase 1
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2808
Polymers104,2532
Non-polymers1,0276
Water13,763764
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5783
Polymers52,1261
Non-polymers4512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7025
Polymers52,1261
Non-polymers5764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.997, 105.466, 193.574
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 Tyrosyl-DNA phosphodiesterase 1 / Tyr-DNA phosphodiesterase 1


Mass: 52126.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP1 / Plasmid: pDN2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-TGM / 4-{[2-(2-hydroxyphenyl)imidazo[1,2-a]pyridin-3-yl]amino}benzene-1,2-dicarboxylic acid


Mass: 389.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.489→50 Å / Num. obs: 165958 / % possible obs: 98.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Rsym value: 0.042 / Net I/σ(I): 40.4
Reflection shellResolution: 1.489→1.52 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 8101 / CC1/2: 0.932 / CC star: 0.982 / Rpim(I) all: 0.163 / Rrim(I) all: 0.406 / Rsym value: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DHU

6dhu


Resolution: 1.489→46.306 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.26
RfactorNum. reflection% reflection
Rfree0.1807 8294 5 %
Rwork0.1506 --
obs0.1522 165842 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.68 Å2 / Biso mean: 26.6565 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.489→46.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6991 0 58 764 7813
Biso mean--37.85 38.4 -
Num. residues----873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.489-1.50590.20912400.1718488892
1.5059-1.52360.22922790.1545511097
1.5236-1.54210.19512740.1452512998
1.5421-1.56170.19532830.134517498
1.5617-1.58220.18622640.1326511098
1.5822-1.60390.19022660.1264519698
1.6039-1.62680.15662870.1231520598
1.6268-1.65110.172550.1229519899
1.6511-1.67690.16182740.1227516498
1.6769-1.70440.17232880.1248514098
1.7044-1.73380.17992710.1325524599
1.7338-1.76530.20132730.1393524299
1.7653-1.79930.19052830.1385524099
1.7993-1.8360.17292560.132516398
1.836-1.87590.17162790.1284522999
1.8759-1.91960.1832930.1326531999
1.9196-1.96760.16852930.1398519599
1.9676-2.02080.16682820.1406530999
2.0208-2.08020.17732350.14615341100
2.0802-2.14740.17592580.14745256100
2.1474-2.22410.16992920.1454527299
2.2241-2.31320.16262800.1469530999
2.3132-2.41840.19382730.1536530599
2.4184-2.54590.1912950.1604526799
2.5459-2.70540.19342760.1608531599
2.7054-2.91430.1982980.17165383100
2.9143-3.20750.20652770.17055375100
3.2075-3.67140.19882850.15975428100
3.6714-4.6250.15622840.1363544099
4.625-46.30.16823010.1714560198

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