6FK4 Dna Binding Protein date Jan 23, 2018
title Structure Of 3' Phosphatase Nexo (Wt) From Neisseria Bound T Substrate
authors J.Silhan, Q.Zhao, E.Boura, H.Thomson, A.Foster, C.M.Tang, P.S.Free G.S.Baldwin
compound source
Molecule: Exodeoxyribonuclease III
Chain: A
Ec: 3.1.11.2
Engineered: Yes
Organism_scientific: Neisseria Meningitidis Serogroup B (St Mc58);
Organism_taxid: 122586
Strain: Mc58
Gene: Xtha, Nmb0399
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Pgpcptpapgpcpgpapapgpcptpa 3');
Chain: B
Engineered: Yes
Other_details: 3' Phosphate Residue At The Last Nucleotide

Synthetic: Yes
Organism_scientific: Other Sequences
Organism_taxid: 28384
symmetry Space Group: P 43 21 2
R_factor 0.199 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.156 59.156 292.091 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MPD enzyme Hydrolase E.C.3.1.11.2 BRENDA
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] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (6fk4.pdb1.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 6FK4
  • CSU: Contacts of Structural Units for 6FK4
  • Structure Factors (945 Kb)
  • Retrieve 6FK4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6FK4 from S2C, [Save to disk]
  • View 6FK4 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 6FK4
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6fk4_B] [6fk4_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6FK4
  • Community annotation for 6FK4 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, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science