MolNFT v1 · #113466 · protein
Crystal structure of the helicase domain of human DNA polymerase theta in complex with amppnp
5AGA: “Crystal structure of the helicase domain of human DNA polymerase theta in complex with amppnp”. X-ray diffraction, 3 ligands (ANP, K, MG), 8 pockets (best druggability 0.84). MolNFT v1 #113466 on GenesisL1: 3D structure, binding…
- 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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