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- PDB-6djh: Crystal structure of Tdp1 catalytic domain in complex with compou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6djh | ||||||
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Title | Crystal structure of Tdp1 catalytic domain in complex with compound XZ515 | ||||||
![]() | Tyrosyl-DNA phosphodiesterase 1 | ||||||
![]() | Hydrolase/Hydrolase Inhibitor / fragment-based drug design / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Burke Jr., T.R. / Pommier, Y. / Waugh, D.S. | ||||||
![]() | ![]() Title: Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Authors: Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.5 KB | Display | ![]() |
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PDB format | ![]() | 162.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dhuC ![]() 6dieC ![]() 6dihC ![]() 6dimC ![]() 6djdC ![]() 6djeC ![]() 6djfC ![]() 6djgC ![]() 6djiC ![]() 6djjC ![]() 6mj5C ![]() 6n17C ![]() 6n19C ![]() 1jy1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 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 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 78029 / % possible obs: 98.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.957 / Num. unique obs: 3767 / CC1/2: 0.754 / Rpim(I) all: 0.343 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JY1 Resolution: 1.918→37.08 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.918→37.08 Å
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Refine LS restraints |
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LS refinement shell |
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