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- PDB-6w7k: Structure of Tdp1 catalytic domain in complex with inhibitor XZ634p -

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Basic information

Entry
Database: PDB / ID: 6w7k
TitleStructure of Tdp1 catalytic domain in complex with inhibitor XZ634p
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 / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / single strand break repair / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA repair / intracellular membrane-bounded organelle ...3'-tyrosyl-DNA phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / single strand break repair / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / DNA repair / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tyrosyl-DNA phosphodiesterase I / Tyrosyl-DNA phosphodiesterase
Similarity search - Domain/homology
Chem-TG7 / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S.
CitationJournal: Chemical Science / Year: 2021
Title: Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites
Authors: Zhao, X.Z. / Kiselev, E. / Lountos, G.T. / Wang, W. / Tropea, J.E. / Needle, D. / Hilimire, T.A. / Schneekloth, J.S. / Waugh, D.S. / Pommier, Y. / Burke, T.R.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 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)105,2488
Polymers104,2532
Non-polymers9956
Water10,683593
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5623
Polymers52,1261
Non-polymers4352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6865
Polymers52,1261
Non-polymers5604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.974, 105.028, 193.590
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-TG7 / 4-[(2-phenylimidazo[1,2-a]pyridin-3-yl)amino]benzene-1,2-dicarboxylic acid


Mass: 373.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15N3O4 / 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.: 593 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
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: 1.7→50 Å / Num. obs: 108780 / % possible obs: 95.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.036 / Rrim(I) all: 0.087 / Rsym value: 0.079 / Net I/σ(I): 26.5
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5192 / CC1/2: 0.714 / CC star: 0.913 / Rpim(I) all: 0.403 / Rrim(I) all: 0.98 / Rsym value: 0.889

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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: 1.7→48.398 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.57
RfactorNum. reflection% reflection
Rfree0.219 5455 5.06 %
Rwork0.187 --
obs0.1886 107820 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.57 Å2 / Biso mean: 26.8934 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.7→48.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 56 593 7649
Biso mean--42.34 35.31 -
Num. residues----875
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.31641760.2668325391
1.7193-1.73960.2911820.2468323793
1.7396-1.76080.27781890.2381331194
1.7608-1.78310.28691610.2398328092
1.7831-1.80650.25281720.2307314990
1.8065-1.83130.26441700.2159318790
1.8313-1.85740.2671840.2102328993
1.8574-1.88520.25981580.2104338595
1.8852-1.91460.23661840.2147342696
1.9146-1.9460.26111910.222332095
1.946-1.97960.26061730.2109338996
1.9796-2.01560.27761610.2066336494
2.0156-2.05430.25781690.2092336095
2.0543-2.09630.2451720.2015337995
2.0963-2.14180.22262000.2036335596
2.1418-2.19170.22181940.2015342196
2.1917-2.24650.22811870.1951341996
2.2465-2.30720.22481750.1964341496
2.3072-2.37510.23181870.1941348296
2.3751-2.45180.22081780.1949339796
2.4518-2.53940.22981860.2009329192
2.5394-2.6410.22822010.1906334594
2.641-2.76120.21211810.194354799
2.7612-2.90680.21791830.198358399
2.9068-3.08890.21732010.1932355599
3.0889-3.32730.20772050.1834360599
3.3273-3.66210.19151840.1709358499
3.6621-4.19170.17132020.14813643100
4.1917-5.28010.16511680.1418349894
5.2801-48.3980.2321810.17983897100

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