Research workbench
Crystal structure of the helicase domain of human DNA polymerase theta in complex with amppnp
Analyse Crystal structure of the helicase domain of human DNA polymerase theta in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AGA
- Type
- protein
- Length
- 785 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
- ANP, K, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase theta (EC 2.7.7.7) | protein | 785 | 49% helix, 12% strand | O75417 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.84 | 0.85 | 112 | empty |
| 2 | 812 | 0.78 | 0.81 | 73 | ANP, MG |
| 3 | 243 | 0.59 | 0.79 | 29 | empty |
| 4 | 183 | 0.51 | 0.77 | 22 | FLC |
| 5 | 73 | 0.47 | 0.83 | 15 | empty |
Compared structures
- 5AGA · Crystal structure of the Helicase domain of human DNA polymerase theta in complex with… · 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 5AGA · PDBe 5AGA · UniProt O75417
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