4NDG Dna Binding Protein Rna Dna date Oct 26, 2013
title Human Aprataxin (Aptx) Bound To Rna-Dna And Zn - Adenosine V Transition State Mimic Complex
authors M.J.Schellenberg, P.S.Tumbale, R.S.Williams
compound source
Molecule: Aprataxin
Chain: A, B
Synonym: Forkhead-Associated Domain Histidine Triad-Like Pr Fha-Hit;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aptx, Axa1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: 5'-R(Pg)-D(Ptptpaptpgpaptptpc)-3'
Chain: D, G
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Gpapaptpcpaptpapapc)-3'
Chain: E, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
40.276 114.580 124.658 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.54 Å
ligand V5A, ZN enzyme
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] (172 Kb) [Save to disk]
  • Biological Unit Coordinates (4ndg.pdb1.gz) 83 Kb
  • Biological Unit Coordinates (4ndg.pdb2.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 4NDG
  • CSU: Contacts of Structural Units for 4NDG
  • Structure Factors (140 Kb)
  • Retrieve 4NDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NDG from S2C, [Save to disk]
  • Re-refined 4ndg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NDG 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 4NDG
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NDG, from MSDmotif at EBI
  • Fold representative 4ndg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ndg_A] [4ndg_G] [4ndg_B] [4ndg_E] [4ndg_D] [4ndg] [4ndg_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NDG: [ZnF_C2H2 ] by SMART
  • Other resources with information on 4NDG
  • Community annotation for 4NDG at PDBWiki (http://pdbwiki.org)

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