6FK5 Dna Binding Protein date Jan 23, 2018
title Structure Of 3' Phosphatase Nexo (D146n) From Neisseria Boun Substrate In Presence Of Magnesium Ion
authors J.Silhan, Q.Zhao, E.Boura, H.Thomson, A.Foster, C.M.Tang, P.S.Free G.S.Baldwin
compound source
Molecule: Nexo D146n
Chain: A
Engineered: Yes
Organism_scientific: Neisseria Meningitidis Mc58
Organism_taxid: 122586
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008

Molecule: Dna (5'-D(Pcptpapgpcpgpapapgpcptpapg
Chain: B
Engineered: Yes
Other_details: 3' Phosphate At The Last Residue

Organism_scientific: Other Sequences
Organism_taxid: 28384
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.230 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.940 58.940 292.260 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.02 Å
ligand MG, MPD enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity


  • Primary referenceStructural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis., Silhan J, Zhao Q, Boura E, Thomson H, Forster A, Tang CM, Freemont PS, Baldwin GS, Nucleic Acids Res. 2018 Oct 17. pii: 5133625. doi: 10.1093/nar/gky934. PMID:30329088
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (6fk5.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 6FK5
  • CSU: Contacts of Structural Units for 6FK5
  • Structure Factors (1511 Kb)
  • Retrieve 6FK5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FK5 from S2C, [Save to disk]
  • View 6FK5 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 6FK5
  • 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
  • Fold representative 6fk5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6fk5_B] [6fk5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FK5
  • Community annotation for 6FK5 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science