Research workbench
Crystal structure of yxag, a dioxygenase from bacillus subtilis
Analyse Crystal structure of yxag, a dioxygenase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y3T
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yxag
- UniProt
- P42106
- Ligands
- FE
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein yxag | protein | 330 | 8% helix, 40% strand | P42106 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 736 | 0.84 | 0.87 | 103 | empty |
| 2 | 226 | 0.75 | 0.89 | 34 | empty |
| 3 | 222 | 0.74 | 0.88 | 34 | empty |
| 4 | 137 | 0.44 | 0.76 | 34 | empty |
| 5 | 74 | 0.42 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1525 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1Y3T · Crystal structure of YxaG, a dioxygenase from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P42106 · AlphaFold monomer V2.0 prediction for quercetin 2,3-dioxygenase (P42106) · 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 P42106
- Elsewhere: RCSB PDB 1Y3T · PDBe 1Y3T · UniProt P42106
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