MolNFT v1 · #61936 · protein
X-ray structure of the complex of regulatory subunits of human DNA polymerase delta
3E0J · DNA polymerase subunit delta-2: “X-ray structure of the complex of regulatory subunits of human DNA polymerase delta”. X-ray diffraction, 20 pockets (best druggability 0.71). MolNFT v1 #61936 on GenesisL1: 3D structure, binding…
- PDB
- 3E0J
- Type
- protein
- Length
- 2,213 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase subunit delta-2; DNA polymerase subunit delta-3
- EC
- 2.7.7.7
- UniProt
- P49005, Q15054
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase subunit delta-2 (EC 2.7.7.7) | protein | 416 | 24% helix, 26% strand | P49005 |
| B, D, F, H | DNA polymerase subunit delta-3 | protein | 143 | 45% helix, 24% strand | Q15054 |
| C | DNA polymerase subunit delta-2 (EC 2.7.7.7) | protein | 409 | 24% helix, 27% strand | P49005 |
| E, G | DNA polymerase subunit delta-2 (EC 2.7.7.7) | protein | 408 | 25% helix, 27% strand | P49005 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.71 | 0.78 | 77 | empty |
| 2 | 61 | 0.70 | 0.96 | 14 | empty |
| 3 | 545 | 0.68 | 0.78 | 59 | empty |
| 4 | 57 | 0.67 | 0.95 | 16 | empty |
| 5 | 669 | 0.67 | 0.76 | 79 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2739 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 2720 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2713 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2710 Ų buried · 41 hydrogen bonds · protein-protein
- C–E · 796 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3E0J · X-ray structure of the complex of regulatory subunits of human DNA polymerase delta · the same entry in another collection · chain H against H, TM-score 1.00
- Q15054 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 3 (Q15054) · a predicted model of the same protein · chain F 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 P49005
- Every structure of UniProt Q15054
- Elsewhere: RCSB PDB 3E0J · PDBe 3E0J · UniProt P49005 · UniProt Q15054
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