Research workbench
Structure of the N-terminal exonuclease domain of the epsilon subunit of E.COLI DNA polymerase III at pH 8.5
Analyse Structure of the N-terminal exonuclease domain of the epsilon subunit of E.COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J53
- Type
- protein
- Length
- 174 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III, epsilon chain
- EC
- 2.7.7.7
- UniProt
- P03007
- Ligands
- TMP, MN
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III, epsilon chain (EC 2.7.7.7) | protein | 174 | 40% helix, 21% strand | P03007 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.55 | 0.78 | 28 | MN, TMP |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 1J53 · Structure of the N-terminal Exonuclease Domain of the Epsilon Subunit of E.coli DNA… · 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
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03007
- Elsewhere: RCSB PDB 1J53 · PDBe 1J53 · UniProt P03007
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