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Yorodumi- PDB-6w7l: Structure of Tdp1 catalytic domain in complex with inhibitor XZ632p -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w7l | ||||||
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Title | Structure of Tdp1 catalytic domain in complex with inhibitor XZ632p | ||||||
Components | Tyrosyl-DNA phosphodiesterase 1 | ||||||
Keywords | HYDROLASE/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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.856 Å | ||||||
Authors | Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w7l.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w7l.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 6w7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w7l ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w7l | HTTPS FTP |
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-Related structure data
Related structure data | 6w7kC 6dhuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52126.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDP1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.11 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.1 M MOPS/HEPES-Na pH 7.5 10% w/v PEG 8000 20% v/v ethylene glycol 0.03M sodium fluoride 0.03M sodium bromide 0.03M sodium iodide PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.856→50 Å / Num. obs: 87892 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.047 / Rrim(I) all: 0.11 / Rsym value: 0.099 / Net I/σ(I): 38.35 |
Reflection shell | Resolution: 1.856→1.89 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4308 / CC1/2: 0.812 / CC star: 0.947 / Rpim(I) all: 0.312 / Rrim(I) all: 0.813 / Rsym value: 0.75 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DHU Resolution: 1.856→48.553 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.85 Å2 / Biso mean: 38.5065 Å2 / Biso min: 17.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.856→48.553 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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