6E3R Dna Binding Protein Dna date Jul 14, 2018
title Structure Of Human Dna Polymerase Beta Complexed With 8oa As Template Base In A 1-Nucleotide Gapped Dna
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(Cpcpgpapcp(A38) Ptpcpgpcpaptpcpapgpc)-3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpa)-3')
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.204 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.572 79.048 54.966 90.00 105.75 90.00
method X-Ray Diffractionresolution 2.26 Å
ligand A38, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases., Koag MC, Jung H, Lee S, J Am Chem Soc. 2019 Mar 20;141(11):4584-4596. doi: 10.1021/jacs.8b08551. Epub, 2019 Mar 7. PMID:30817143
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (6e3r.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 6E3R
  • CSU: Contacts of Structural Units for 6E3R
  • Structure Factors (432 Kb)
  • Retrieve 6E3R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6E3R from S2C, [Save to disk]
    • View 6E3R 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 6E3R
  • 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: [6e3r_T] [6e3r_P] [6e3r_D] [6e3r_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6E3R
  • Community annotation for 6E3R at PDBWiki (http://pdbwiki.org)

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