Research workbench
Ternary crystal structure of yeast DNA polymerase epsilon with template G
Analyse Ternary crystal structure of yeast DNA polymerase epsilon with template G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PTF
- Type
- protein + DNA
- Length
- 1,138 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon catalytic subunit a; 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))…
- EC
- 2.7.7.7
- UniProt
- P21951
- Ligands
- DCP, CA, NA
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 1112 | 42% helix, 22% strand | P21951 |
| P | 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3' | dna | 11 | — | — |
| T | 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3' | dna | 15 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
- CA · Calcium ion · metal · 4 copies · chains A, P, T
- NA · Sodium ion · metal · chains A, T
- EDO · 1,2-ethanediol · additive · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.78 | 0.83 | 62 | DCP, CA |
| 2 | 383 | 0.75 | 0.86 | 48 | NA |
| 3 | 821 | 0.73 | 0.78 | 73 | CA |
| 4 | 166 | 0.52 | 0.79 | 31 | empty |
| 5 | 82 | 0.52 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1327 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–P · 753 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 492 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4PTF · Ternary crystal structure of yeast DNA polymerase epsilon with template G · the same entry in another collection · chain A against A, 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 4PTF · PDBe 4PTF · UniProt P21951
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