5DB6 Transferase Dna date Aug 20, 2015
title Structure Of Human Dna Polymerase Beta Host-Guest Complex Wi N7mg Base Paired With A Dc
authors M.C.Koag, S.Lee
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Cpcpgpapcpgptpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcptp(Fmg)Paptpgpcpgpa)-3')
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.185 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.138 78.828 54.764 90.00 105.92 90.00
method X-Ray Diffractionresolution 2.83 Å
ligand FMG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceN7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA., Kou Y, Koag MC, Lee S, J Am Chem Soc. 2015 Nov 11;137(44):14067-70. doi: 10.1021/jacs.5b10172. Epub 2015, Nov 2. PMID:26517568
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (5db6.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 5DB6
  • CSU: Contacts of Structural Units for 5DB6
  • Structure Factors (94 Kb)
  • Retrieve 5DB6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DB6 from S2C, [Save to disk]
  • Re-refined 5db6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DB6 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 5DB6
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5db6_T] [5db6] [5db6_D] [5db6_A] [5db6_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DB6: [HhH1] [POLXc ] by SMART
    • Other resources with information on 5DB6
  • Community annotation for 5DB6 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