[English] 日本語
Yorodumi- PDB-3c49: Human poly(ADP-ribose) polymerase 3, catalytic fragment in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c49 | ||||||
---|---|---|---|---|---|---|---|
Title | Human poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor KU0058948 | ||||||
Components | Poly(ADP-ribose) polymerase 3 | ||||||
Keywords | TRANSFERASE / enzyme-inhibitor complex / catalytic fragment / Structural Genomics / Structural Genomics Consortium / SGC / Alternative splicing / Glycosyltransferase / NAD / Nucleus | ||||||
Function / homology | Function and homology information negative regulation of isotype switching / : / NAD+-protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation ...negative regulation of isotype switching / : / NAD+-protein-lysine ADP-ribosyltransferase activity / positive regulation of DNA ligation / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / protein localization to site of double-strand break / protein auto-ADP-ribosylation / intercellular bridge / positive regulation of double-strand break repair via nonhomologous end joining / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / catalytic activity / regulation of mitotic spindle organization / centriole / telomere maintenance / nucleotidyltransferase activity / double-strand break repair / site of double-strand break / nuclear body / centrosome / nucleolus / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Lehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Lehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Helleday, T. / Herman, M.D. / Johansson, A. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van den Berg, S. / Welin, M. / Weigelt, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3. Authors: Lehtio, L. / Jemth, A.S. / Collins, R. / Loseva, O. / Johansson, A. / Markova, N. / Hammarstrom, M. / Flores, A. / Holmberg-Schiavone, L. / Weigelt, J. / Helleday, T. / Schuler, H. / Karlberg, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3c49.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3c49.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 3c49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c49_validation.pdf.gz | 783.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3c49_full_validation.pdf.gz | 786.6 KB | Display | |
Data in XML | 3c49_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3c49_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c49 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c49 | HTTPS FTP |
-Related structure data
Related structure data | 3c4hC 3ce0C 3fhbC 2pa9 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39752.074 Da / Num. of mol.: 1 / Fragment: Catalytic fragment: Residues 178-532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP3, ADPRT3, ADPRTL3 / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6F1, NAD+ ADP-ribosyltransferase |
---|---|
#2: Chemical | ChemComp-KU8 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M DL-Malic acid, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 8076 / Num. obs: 8076 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.33 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.97 / Num. unique all: 798 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PA9 2pa9 Resolution: 2.8→20 Å / Isotropic thermal model: grouped isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.12 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|