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Structure and function of cyclized versions of the proofreading exonuclease subunit of E. COLI DNA polymerase III

Analyse Structure and function of cyclized versions of the proofreading exonuclease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2GUI
Type
protein
Length
176 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase III epsilon subunit
EC
2.7.7.7
UniProt
P03007
Ligands
U5P, MN
Pockets
1 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA polymerase III epsilon subunit (EC 2.7.7.7)protein17640% helix, 19% strandP03007

Ligands and binding sites

  • U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A
  • MN · Manganese (II) ion · metal · 2 copies · chains A
  • EDO · 1,2-ethanediol · additive · 2 copies · chains A
  • PEG · Di(hydroxyethyl)ether · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12180.560.7929MN, U5P

Compared structures

  • 2GUI · Structure and Function of Cyclized Versions of the Proofreading Exonuclease Subunit of E.… · the same entry in another collection · chain A against A, TM-score 1.00
  • P03007 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit epsilon (P03007) · a predicted model of the same protein · chain A against A, TM-score 0.99

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