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Open data
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Basic information
Entry | Database: PDB / ID: 4tvj | ||||||
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Title | HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB | ||||||
![]() | Poly [ADP-ribose] polymerase 2 | ||||||
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Function / homology | ![]() hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) ...hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) / poly-ADP-D-ribose modification-dependent protein binding / DNA repair-dependent chromatin remodeling / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karlberg, T. / Thorsell, A.G. / Ekblad, T. / Pinto, A.F. / Schuler, H. | ||||||
![]() | ![]() Title: Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors. Authors: Thorsell, A.G. / Ekblad, T. / Karlberg, T. / Low, M. / Pinto, A.F. / Tresaugues, L. / Moche, M. / Cohen, M.S. / Schuler, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.5 KB | Display | ![]() |
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PDB format | ![]() | 236.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4r5wC ![]() 4r6eC ![]() 4rv6C ![]() 4undC ![]() 4uxbC ![]() 5lx6C ![]() 3kczS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41827.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Sequence details | The sequence mismatch is due to sequence conflicts between Uniprot and GenBank (ID AF085734.1). In ...The sequence mismatch is due to sequence conflicts between Uniprot and GenBank (ID AF085734.1). In this case authors have used the sequence from GenBank (http://www.ncbi.nlm.nih.gov/nuccore/4808556), here residue 447 is Histidine. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% PEG3350, 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→30 Å / Num. all: 45851 / Num. obs: 45851 / % possible obs: 99.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.107 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.1 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3KCZ Resolution: 2.1→29.28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.101 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.879 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→29.28 Å
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