6MR8 Dna Binding Protein Dna date Oct 11, 2018
title D276g Dna Polymerase Beta Substrate Complex With Templating And Incoming Fapy-Dgtp Analog
authors B.D.Freudenthal, M.R.Smith, S.H.Wilson, W.A.Beard
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(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.015 80.282 55.564 90.00 110.46 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CA, EDO, GKS, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA guardian residue hinders insertion of a Fapy*dGTP analog by modulating the open-closed DNA polymerase transition., Smith MR, Shock DD, Beard WA, Greenberg MM, Freudenthal BD, Wilson SH, Nucleic Acids Res. 2019 Jan 16. pii: 5289696. doi: 10.1093/nar/gkz002. PMID:30649431
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (6mr8.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 6MR8
  • CSU: Contacts of Structural Units for 6MR8
  • Structure Factors (421 Kb)
  • Retrieve 6MR8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6MR8 from S2C, [Save to disk]
  • View 6MR8 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 6MR8
  • 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 6mr8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6mr8_A] [6mr8_D] [6mr8_P] [6mr8_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6MR8
  • Community annotation for 6MR8 at PDBWiki (http://pdbwiki.org)

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