4NDI Human Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and Zn - product complex date 2013-10-26
authors Schellenberg, M.J., Tumbale, P.S., Williams, R.S.
compound source
symmetry
R_factor
R_Free 0.1817
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.90
ligand AMP, BME, GOL, K, NA, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceAprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity., Tumbale P, Williams JS, Schellenberg MJ, Kunkel TA, Williams RS, Nature. 2013 Dec 22. doi: 10.1038/nature12824. PMID:24362567
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (181 Kb) [Save to disk]
  • Biological Unit Coordinates (4ndi.pdb1.gz) 88 Kb
  • Biological Unit Coordinates (4ndi.pdb2.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 4NDI
  • CSU: Contacts of Structural Units for 4NDI
  • Structure Factors (335 Kb)
  • Retrieve 4NDI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NDI from S2C, [Save to disk]
  • Re-refined 4ndi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NDI in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4NDI
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4NDI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ndi_D] [4ndi_H] [4ndi_B] [4ndi_G] [4ndi_A] [4ndi] [4ndi_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NDI: [ZnF_C2H2 ] by SMART
  • Other resources with information on 4NDI
  • Community annotation for 4NDI at PDBWiki (http://pdbwiki.org)

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