MolNFT v1 · #113245 · protein
Crystal structure of the helicase domain of human DNA polymerase theta in complex with ADP
5A9F: “Crystal structure of the helicase domain of human DNA polymerase theta in complex with ADP”. X-ray diffraction, 3 ligands (ADP, K, MG), 11 pockets (best druggability 0.80). MolNFT v1 #113245 on GenesisL1: 3D structure, binding sites…
- PDB
- 5A9F
- Type
- protein
- Length
- 780 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase theta
- EC
- 2.7.7.7
- UniProt
- O75417
- Ligands
- ADP, K, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase theta (EC 2.7.7.7) | protein | 780 | 48% helix, 12% strand | O75417 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.80 | 0.86 | 63 | empty |
| 2 | 562 | 0.77 | 0.83 | 60 | ADP, MG |
| 3 | 401 | 0.74 | 0.84 | 48 | empty |
| 4 | 264 | 0.60 | 0.79 | 30 | empty |
| 5 | 208 | 0.54 | 0.78 | 20 | empty |
Compared structures
- 5A9F · Crystal structure of the Helicase domain of human DNA polymerase theta in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- O75417 · AlphaFold monomer V2.0 prediction for DNA polymerase theta (O75417) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5A9F · PDBe 5A9F · UniProt O75417
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