Research workbench
Crystal structure of the Helicase domain of human DNA polymerase theta, apo-form
Analyse Crystal structure of the Helicase domain of human DNA polymerase theta, apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A9J
- Type
- protein
- Length
- 3,158 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.55
- Source
- HOMO SAPIENS
- Molecule
- DNA polymerase theta
- UniProt
- O75417
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.55 · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase theta | protein | 805 | 50% helix, 11% strand | O75417 |
| B | DNA polymerase theta | protein | 801 | 50% helix, 12% strand | O75417 |
| C | DNA polymerase theta | protein | 780 | 49% helix, 12% strand | O75417 |
| D | DNA polymerase theta | protein | 772 | 50% helix, 12% strand | O75417 |
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 | 982 | 0.84 | 0.85 | 98 | empty |
| 2 | 913 | 0.83 | 0.84 | 90 | empty |
| 3 | 921 | 0.82 | 0.84 | 92 | empty |
| 4 | 681 | 0.81 | 0.85 | 66 | empty |
| 5 | 820 | 0.80 | 0.83 | 64 | empty |
Interfaces
6 interfaces between chains.
- B–D · 919 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 864 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 846 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 645 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5A9J · Crystal structure of the helicase domain of human DNA polymerase theta, apo-form · the same entry in another collection · chain D against D, TM-score 1.00
- O75417 · AlphaFold monomer V2.0 prediction for DNA polymerase theta (O75417) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 O75417
- Elsewhere: RCSB PDB 5A9J · PDBe 5A9J · UniProt O75417
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