MolNFT v1 · #54736 · protein
Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III
2XY8 · DNA polymerase III subunit epsilon: “Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain…”. Solution nmr, 1 ligand (CA), 1 pocket (best druggability 0.65). MolNFT v1 #54736 on…
- PDB
- 2XY8
- Type
- protein
- Length
- 235 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III subunit epsilon; DNA polymerase III subunit theta
- EC
- 2.7.7.7
- UniProt
- P03007, P0ABT0
- Ligands
- CA
- Pockets
- 1 · best druggability 0.65
Structure
solution nmr · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III subunit epsilon (EC 2.7.7.7) | protein | 174 | 37% helix, 18% strand | P03007 |
| B | DNA polymerase III subunit theta (EC 2.7.7.7) | protein | 61 | 72% helix, 0% strand | P0ABT0 |
Ligands and binding sites
- CA · Calcium ion · metal · 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 | 493 | 0.65 | 0.77 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 867 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2XY8 · Paramagnetic-based NMR structure of the complex between the N- terminal epsilon domain… · 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 0.96
- P0ABT0 · AlphaFold monomer V2.0 prediction for DNA polymerase III subunit theta (P0ABT0) · a predicted model of the same protein · chain B against A, TM-score 0.70
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
- Every structure of UniProt P0ABT0
- Elsewhere: RCSB PDB 2XY8 · PDBe 2XY8 · UniProt P03007 · UniProt P0ABT0
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