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The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.
Analyse The crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I8A
- Type
- protein + DNA
- Length
- 2,253 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.652
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c); SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase epsilon catalytic subunit A; Primer DNA; Template DNA
- EC
- 2.7.7.7
- UniProt
- P21951
- Ligands
- DTP, CA, FE
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.652 · 4 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon catalytic subunit A (EC 2.7.7.7) | protein | 1107 | 42% helix, 22% strand | P21951 |
| P, C | Primer DNA | dna | 11 | — | — |
| T, D | Template DNA | dna | 15 | — | — |
| B | DNA polymerase epsilon catalytic subunit A (EC 2.7.7.7) | protein | 1094 | 43% helix, 22% strand | P21951 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, P, T, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.79 | 0.81 | 90 | DTP |
| 2 | 1068 | 0.75 | 0.78 | 68 | DTP |
| 3 | 464 | 0.71 | 0.82 | 50 | empty |
| 4 | 983 | 0.71 | 0.75 | 71 | CA |
| 5 | 78 | 0.70 | 0.95 | 28 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1246 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–T · 1238 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 748 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 681 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–T · 496 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6I8A · The crystal structure of the POL2 catalytic domain of DNA polymerase epsilon carrying a… · the same entry in another collection · chain T against T, TM-score 1.00
- P21951 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (P21951) · 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 P21951
- Elsewhere: RCSB PDB 6I8A · PDBe 6I8A · UniProt P21951
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