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- PDB-9b3b: Structure of TDP1 complexed with compound IB09 -

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Basic information

Entry
Database: PDB / ID: 9b3b
TitleStructure of TDP1 complexed with compound IB09
ComponentsTyrosyl-DNA phosphodiesterase 1
KeywordsDNA BINDING PROTEIN / phosphodiesterase / drug target / cancer
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
: / Tyrosyl-DNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLountos, G.T. / Zhao, X.Z. / Barakat, I. / Wang, W. / Agama, K. / Al Mahmud, M.R. / Pommier, Y. / Burke, T.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Structure of TDP1 complexed with compound IB09
Authors: Lountos, G.T. / Zhao, X.Z. / Barakat, I. / Wang, W. / Agama, K. / Al Mahmud, M.R. / Pommier, Y. / Burke, T.R.
History
DepositionMar 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)105,82013
Polymers104,2532
Non-polymers1,56811
Water13,601755
1
A: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0118
Polymers52,1261
Non-polymers8857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosyl-DNA phosphodiesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8095
Polymers52,1261
Non-polymers6834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.023, 104.748, 193.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Details (production host): pDN2454 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical ChemComp-A1AIM / (8M)-8-{4-(benzylcarbamoyl)-2-[(fluorosulfonyl)oxy]phenyl}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid


Mass: 496.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H17FN2O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MOPS/HEPES pH 7.5, 10% (w/v) PEG 8000, 20% (w/v) ethylene glycol, 0.03M sodium fluoride, 0.03 M sodium bromide, 0.03 sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 122336 / % possible obs: 94.2 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rsym value: 0.061 / Net I/σ(I): 24.7
Reflection shellResolution: 1.62→1.65 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5701 / CC1/2: 0.803 / Rpim(I) all: 0.297 / Rsym value: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→45.14 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 6062 4.96 %
Rwork0.1601 --
obs0.1616 122247 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6969 0 90 755 7814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187651
X-RAY DIFFRACTIONf_angle_d1.44310465
X-RAY DIFFRACTIONf_dihedral_angle_d5.8556023
X-RAY DIFFRACTIONf_chiral_restr0.1021085
X-RAY DIFFRACTIONf_plane_restr0.0111340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.28591800.21883540X-RAY DIFFRACTION88
1.6384-1.65760.23471810.213664X-RAY DIFFRACTION90
1.6576-1.67790.24911680.19333615X-RAY DIFFRACTION88
1.6779-1.69910.21441830.18453645X-RAY DIFFRACTION90
1.6991-1.72150.20511860.18363678X-RAY DIFFRACTION90
1.7215-1.7450.22851940.17853709X-RAY DIFFRACTION92
1.745-1.770.2011920.17443708X-RAY DIFFRACTION91
1.77-1.79640.19322150.16753666X-RAY DIFFRACTION90
1.7964-1.82450.21381930.16763712X-RAY DIFFRACTION92
1.8245-1.85440.20251760.16453762X-RAY DIFFRACTION91
1.8544-1.88630.22632040.16683732X-RAY DIFFRACTION93
1.8863-1.92060.18372240.16753776X-RAY DIFFRACTION93
1.9206-1.95760.19151760.15993793X-RAY DIFFRACTION92
1.9576-1.99750.18882000.1533851X-RAY DIFFRACTION94
1.9975-2.0410.18411740.15683791X-RAY DIFFRACTION93
2.041-2.08850.17862230.1593816X-RAY DIFFRACTION93
2.0885-2.14070.21771920.15393507X-RAY DIFFRACTION86
2.1407-2.19860.18592160.15423839X-RAY DIFFRACTION94
2.1986-2.26330.22160.15344012X-RAY DIFFRACTION97
2.2633-2.33630.18362280.15763963X-RAY DIFFRACTION97
2.3363-2.41980.17932360.15964040X-RAY DIFFRACTION98
2.4198-2.51670.19552250.16044066X-RAY DIFFRACTION99
2.5167-2.63120.19992060.16124137X-RAY DIFFRACTION100
2.6312-2.76990.19882070.16094107X-RAY DIFFRACTION100
2.7699-2.94340.19731900.16284158X-RAY DIFFRACTION100
2.9434-3.17060.1732270.16384128X-RAY DIFFRACTION100
3.1706-3.48960.17182190.15524146X-RAY DIFFRACTION100
3.4896-3.99430.17152010.14663993X-RAY DIFFRACTION95
3.9943-5.03130.16452120.13384207X-RAY DIFFRACTION98
5.0313-45.140.19582180.18044424X-RAY DIFFRACTION100
Refinement TLS params.

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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4728-0.230.37550.711-0.26171.7487-0.076-0.10860.09450.03160.03740.0747-0.0745-0.24740.01960.08770.0088-0.00530.06260.01120.1492.0651-2.1867-42.7616
21.26930.0650.57640.3851-0.19671.32030.0630.0476-0.173-0.0279-0.0388-0.0370.30990.1090.02190.14840.0178-0.00070.05330.00860.170218.7825-16.807-43.4416
31.855-0.1084-0.0110.4452-0.19314.12880.0291-0.01890.02230.152-0.1261-0.0345-0.12190.24850.06420.0863-0.007-0.0050.10810.01590.177124.2823-9.8365-34.69
41.9510.27150.83520.16890.45671.8848-0.1890.09430.51120.0118-0.2697-0.1047-0.72360.10280.2220.2491-0.0399-0.04330.19390.14550.28014.524116.9104-85.8263
51.6222-0.19530.33910.9896-0.39991.8067-0.06660.31940.1466-0.0662-0.1904-0.2489-0.06870.69790.11540.1092-0.01140.01440.33720.15080.220516.83377.4606-85.532
61.15380.06080.60730.4861-0.1732.60760.0908-0.0104-0.2485-0.0578-0.0574-0.03940.5821-0.0525-0.02120.2010.01390.01610.12150.03920.1835-0.6034-7.139-86.5008
71.34540.302-0.64710.5407-0.83555.4155-0.0317-0.0277-0.038-0.05850.02050.0478-0.0232-0.46780.01560.08850.0185-0.00710.20420.01550.1651-8.51242.4635-95.2238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 162 through 382 )
2X-RAY DIFFRACTION2chain 'A' and (resid 383 through 548 )
3X-RAY DIFFRACTION3chain 'A' and (resid 549 through 607 )
4X-RAY DIFFRACTION4chain 'B' and (resid 162 through 202 )
5X-RAY DIFFRACTION5chain 'B' and (resid 203 through 344 )
6X-RAY DIFFRACTION6chain 'B' and (resid 345 through 548 )
7X-RAY DIFFRACTION7chain 'B' and (resid 549 through 607 )

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