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Yorodumi- PDB-5nqe: Human PARP14 (ARTD8), catalytic fragment in complex with an N-ary... -
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-Basic information
Entry | Database: PDB / ID: 5nqe | ||||||
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Title | Human PARP14 (ARTD8), catalytic fragment in complex with an N-aryl piperazine inhibitor | ||||||
Components | Poly [ADP-ribose] polymerase 14 | ||||||
Keywords | TRANSFERASE / ADP-ribosylation / Inhibitor complex / Transferase domain | ||||||
Function / homology | Function and homology information positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Karlberg, T. / Thorsell, A.G. / Schuler, H. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14. Authors: Upton, K. / Meyers, M. / Thorsell, A.G. / Karlberg, T. / Holechek, J. / Lease, R. / Schey, G. / Wolf, E. / Lucente, A. / Schuler, H. / Ferraris, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nqe.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nqe.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/5nqe ftp://data.pdbj.org/pub/pdb/validation_reports/nq/5nqe | HTTPS FTP |
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-Related structure data
Related structure data | 4f1lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22118.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP14, BAL2, KIAA1268 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 3.06 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Sodium-malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→45.2 Å / Num. all: 97208 / Num. obs: 14476 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 63.32 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.288 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.71→2.87 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14938 / CC1/2: 0.641 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F1L Resolution: 2.71→45.18 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.869 / SU R Cruickshank DPI: 0.681 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.597 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.319
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Displacement parameters | Biso mean: 40.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.71→45.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.93 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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