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- PDB-2pax: THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pax | ||||||
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Title | THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH 4-AMINO-1,8-NAPHTHALIMIDE | ||||||
![]() | POLY(ADP-RIBOSE) POLYMERASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / NAD(+) ADP-RIBOSYLTRANSFERASE / DNA-BINDING | ||||||
Function / homology | ![]() NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation ...NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+-protein poly-ADP-ribosyltransferase activity / nucleosome binding / negative regulation of innate immune response / nucleotidyltransferase activity / NAD binding / double-strand break repair / site of double-strand break / damaged DNA binding / innate immune response / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ruf, A. / Schulz, G.E. | ||||||
![]() | ![]() Title: Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling. Authors: Ruf, A. / de Murcia, G. / Schulz, G.E. #1: ![]() Title: Structure of the Catalytic Fragment of Poly(Ad-Ribose) Polymerase from Chicken Authors: Ruf, A. / Mennissier De Murcia, J. / De Murcia, G.M. / Schulz, G.E. #2: ![]() Title: Crystallization and X-Ray Crystallographic Analysis of Recombinant Chicken Poly(Adp-Ribose) Polymerase Catalytic Domain Produced in Sf9 Insect Cells Authors: Jung, S. / Miranda, E.A. / De Murcia, J.M. / Niedergang, C. / Delarue, M. / Schulz, G.E. / De Murcia, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.3 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.7 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pawC ![]() 3paxC ![]() 4paxC ![]() 1paxS 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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Unit cell |
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Components
#1: Protein | Mass: 40415.352 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-4AN / |
#3: Water | ChemComp-HOH / |
Sequence details | HUMAN SEQUENCE NUMBERS ARE USED THROUGHOUT INSTEAD OF CHICKEN NUMBERS TO FACILITATE COMPARISON WITH ...HUMAN SEQUENCE NUMBERS ARE USED THROUGHOUT |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG 600, 6% ISOPROPANOL, 100 MM TRIS, PH 8.5 AND 0.03MM 4-AMINO-1,8-NAPHTALIMIDE | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15.1 Å / Num. obs: 13590 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 7.3 / Rsym value: 0.232 / % possible all: 73.3 |
Reflection | *PLUS % possible obs: 95 % / Num. measured all: 49815 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 73 % / Rmerge(I) obs: 0.232 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1PAX Resolution: 2.4→15.1 Å / σ(F): 0 / Details: X-PLOR BULK SOLVENT CORRECTION WAS APPLIED.
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Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2716 |