Research workbench
Crystal structure of uracil-DNA glycosylase from thermus thermophilus HB8
Analyse Crystal structure of uracil-DNA glycosylase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D3Y
- Type
- protein
- Length
- 219 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase
- EC
- 3.2.2.-
- UniProt
- Q5SJ65
- Ligands
- SF4, DU
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.-) | protein | 219 | 39% helix, 13% strand | Q5SJ65 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- DU · 2'-deoxyuridine-5'-monophosphate · ligand · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.65 | 0.82 | 45 | ACT |
| 2 | 55 | 0.31 | 0.76 | 14 | empty |
Compared structures
- 2D3Y · Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SJ65 · AlphaFold monomer V2.0 prediction for type-5 uracil-DNA glycosylase (Q5SJ65) · a predicted model of the same protein · chain A 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 Q5SJ65
- Elsewhere: RCSB PDB 2D3Y · PDBe 2D3Y · UniProt Q5SJ65
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.