4QZD Transferase Dna date Jul 27, 2014
title Mouse Tdt, F405a Mutant, In Complex With A Dsb Substrate, C- Pair
authors J.Gouge, M.Delarue
compound source
Molecule: Dna Nucleotidylexotransferase
Chain: A
Fragment: See Remark 999
Synonym: Terminal Addition Enzyme, Terminal Deoxynucleotidyltransferase, Tdt, Terminal Transferase;
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Dntt, Tdt
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Apapapapapc)-3'
Chain: D, U
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tptptptptpgpc)-3'
Chain: T
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.200 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
55.933 74.920 125.633 90.00 98.43 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand DCT, MG, NA enzyme Transferase E.C. BRENDA

Primary referenceStructural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair., Gouge J, Rosario S, Romain F, Poitevin F, Beguin P, Delarue M, EMBO J. 2015 Apr 15;34(8):1126-42. doi: 10.15252/embj.201489643. Epub 2015 Mar, 11. PMID:25762590
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (4qzd.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 4QZD
  • CSU: Contacts of Structural Units for 4QZD
  • Structure Factors (776 Kb)
  • Retrieve 4QZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QZD from S2C, [Save to disk]
  • Re-refined 4qzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4QZD 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 4QZD
  • 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 4QZD, from MSDmotif at EBI
  • Fold representative 4qzd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qzd] [4qzd_U] [4qzd_D] [4qzd_T] [4qzd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4QZD: [POLXc ] by SMART
  • Other resources with information on 4QZD
  • Community annotation for 4QZD at PDBWiki (http://pdbwiki.org)

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