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- PDB-3vfq: Human PARP14 (ARTD8, BAL2) - macro domains 1 and 2 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vfq | ||||||
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Title | Human PARP14 (ARTD8, BAL2) - macro domains 1 and 2 in complex with adenosine-5-diphosphoribose | ||||||
![]() | Poly [ADP-ribose] polymerase 14 | ||||||
![]() | TRANSFERASE / ADP-RIBOSE / PARP14 / MACRO / BAL2 / ARTD8 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() 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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity ...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 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karlberg, T. / Thorsell, A.G. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Ekblad, T. / Weigelt, J. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Recognition of Mono-ADP-Ribosylated ARTD10 Substrates by ARTD8 Macrodomains. Authors: Forst, A.H. / Karlberg, T. / Herzog, N. / Thorsell, A.G. / Gross, A. / Feijs, K.L. / Verheugd, P. / Kursula, P. / Nijmeijer, B. / Kremmer, E. / Kleine, H. / Ladurner, A.G. / Schuler, H. / Luscher, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.9 KB | Display | ![]() |
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Full document | ![]() | 751.7 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q6zSC ![]() 3q71SC ![]() 3v2bC ![]() 4abkC ![]() 4ablC ![]() 4d86C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44707.414 Da / Num. of mol.: 1 / Fragment: Macro domains 1 and 2 (UNP residues 784-1196) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-AR6 / [( |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 0.2M SODIUM-THIOCYANATE, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2010 |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93928 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 10514 / Num. obs: 10514 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.175 / Rsym value: 0.132 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 2.3 / Num. unique all: 750 / Rsym value: 0.652 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3Q6Z AND 3Q71 Resolution: 2.8→46.62 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.454 / 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 |
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Refinement step | Cycle: LAST / Resolution: 2.8→46.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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