MolNFT v1 · #137030 · protein
Crystal structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit
5VBN · DNA polymerase epsilon subunit 2: “Crystal structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic…”. X-ray diffraction, 2 ligands (ZN, SO4), 11 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 5VBN
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon subunit 2; DNA polymerase epsilon catalytic subunit a
- EC
- 2.7.7.7
- UniProt
- P56282, Q07864
- Ligands
- ZN, SO4
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | DNA polymerase epsilon subunit 2 (EC 2.7.7.7) | protein | 427 | 30% helix, 30% strand | P56282 |
| B, F | DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7) | protein | 125 | 41% helix, 19% strand | Q07864 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.61 | 0.81 | 24 | empty |
| 2 | 220 | 0.59 | 0.80 | 25 | empty |
| 3 | 269 | 0.53 | 0.75 | 48 | empty |
| 4 | 173 | 0.50 | 0.77 | 29 | empty |
| 5 | 174 | 0.48 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- E–F · 1647 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 731 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5VBN · Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal… · the same entry in another collection · chain F against F, TM-score 1.00
- P56282 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon subunit 2 (P56282) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q07864 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (Q07864) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P56282
- Every structure of UniProt Q07864
- Elsewhere: RCSB PDB 5VBN · PDBe 5VBN · UniProt P56282 · UniProt Q07864
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