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- PDB-8hks: Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hks | ||||||||||||
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Title | Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) | ||||||||||||
![]() | Poly [ADP-ribose] polymerase 2 | ||||||||||||
![]() | TRANSFERASE / DNA ADP-ribosyltransferase 2 / PARP2 / Pamiparib / BGB-290 | ||||||||||||
Function / homology | ![]() response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / 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 / poly-ADP-D-ribose modification-dependent protein binding ...response to oxygen-glucose deprivation / hippocampal neuron apoptotic process / 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 / poly-ADP-D-ribose modification-dependent protein binding / HDR through MMEJ (alt-NHEJ) / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / extrinsic apoptotic signaling pathway / nucleosome binding / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wang, X.Y. / Zhou, J. / Xu, B.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib Authors: Wang, X.Y. / Zhou, J. / Xu, B.L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.4 KB | Display | ![]() |
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PDB format | ![]() | 232.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 51.5 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39965.910 Da / Num. of mol.: 4 / Mutation: T349S,L351R,S353G,P354L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-DS9 / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 25% PEG-3350, 0.1 M Tris-HCl pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→95.77 Å / Num. obs: 31716 / % possible obs: 94.78 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.46 Å2 / CC1/2: 0.994 / Net I/σ(I): 16.27 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 2855 / CC1/2: 0.861 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Alphafold model Resolution: 2.8→95.77 Å / SU ML: 0.2945 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.6053 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→95.77 Å
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Refine LS restraints |
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LS refinement shell |
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