Research workbench
Structure of the E. COLI pol III epsilon-hot proofreading complex
Analyse Structure of the E. COLI pol III epsilon-hot proofreading complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IDO
- Type
- protein
- Length
- 498 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III epsilon subunit; Hot protein
- EC
- 2.7.7.7
- UniProt
- P03007, Q71T70
- Ligands
- TMP, MN
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III epsilon subunit (EC 2.7.7.7) | protein | 172 | 41% helix, 19% strand | P03007 |
| B | Hot protein | protein | 75 | 71% helix, 0% strand | Q71T70 |
| C | DNA polymerase III epsilon subunit (EC 2.7.7.7) | protein | 175 | 41% helix, 18% strand | P03007 |
| D | Hot protein | protein | 76 | 67% helix, 0% strand | Q71T70 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 5 copies · chains A, C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.72 | 0.79 | 56 | MN, TMP, EDO |
| 2 | 230 | 0.54 | 0.77 | 31 | MN, TMP |
| 3 | 227 | 0.52 | 0.76 | 35 | MN |
| 4 | 201 | 0.49 | 0.75 | 31 | empty |
| 5 | 75 | 0.36 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1014 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 682 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2IDO · Structure of the E. coli Pol III epsilon-Hot proofreading complex · 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
- Every structure of UniProt Q71T70
- Elsewhere: RCSB PDB 2IDO · PDBe 2IDO · UniProt P03007 · UniProt Q71T70
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