MolNFT v1 · #151689 · protein
Cryo-EM structure of S. cerevisiae polymerase epsilon deltacat mutant
6HV8 · DNA polymerase epsilon subunit B: “Cryo-EM structure of S. cerevisiae polymerase epsilon deltacat mutant”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.80). MolNFT v1 #151689 on GenesisL1: 3D structure…
- PDB
- 6HV8
- Type
- protein
- Length
- 1,184 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon subunit B; DNA polymerase epsilon catalytic subunit a
- EC
- 2.7.7.7
- UniProt
- P24482, P21951
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 28% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase epsilon subunit B (EC 2.7.7.7) | protein | 410 | 25% helix, 22% strand | P24482 |
| A | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 774 | 30% helix, 5% strand | P21951 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.80 | 0.88 | 67 | empty |
| 2 | 688 | 0.78 | 0.83 | 56 | empty |
| 3 | 781 | 0.78 | 0.82 | 96 | empty |
| 4 | 984 | 0.77 | 0.79 | 92 | empty |
| 5 | 554 | 0.73 | 0.81 | 76 | empty |
Interfaces
1 interface between chains.
- B–A · 2336 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6HV8 · Cryo-EM structure of S. cerevisiae Polymerase epsilon deltacat mutant · the same entry in another collection · chain B against B, TM-score 1.00
- P24482 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon subunit B (P24482) · a predicted model of the same protein · chain B against A, TM-score 0.95
- 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 0.91
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 P24482
- Every structure of UniProt P21951
- Elsewhere: RCSB PDB 6HV8 · PDBe 6HV8 · UniProt P24482 · UniProt P21951
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