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MolNFT v1 · #38349 · protein

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

2GUI · DNA polymerase III epsilon subunit: “Structure and function of cyclized versions of the proofreading exonuclease subunit of E. COLI DNA polymerase…”. X-ray diffraction, 2 ligands (U5P, MN), 1 pocket (best druggability 0.56). MolNFT…

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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