Research workbench
Structure of the substrate-free FAD-dependent tirandamycin oxidase taml
Analyse Structure of the substrate-free FAD-dependent tirandamycin oxidase taml in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y08
- Type
- protein
- Length
- 998 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Taml
- UniProt
- D3Y1I2
- Ligands
- FAD, MG, CL
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taml | protein | 498 | 33% helix, 21% strand | D3Y1I2 |
| B | Taml | protein | 500 | 32% helix, 21% strand | D3Y1I2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.84 | 0.93 | 70 | FAD, GOL |
| 2 | 409 | 0.84 | 0.92 | 80 | MG, CL |
| 3 | 289 | 0.83 | 0.94 | 52 | FAD |
| 4 | 127 | 0.76 | 0.95 | 42 | MG |
| 5 | 84 | 0.60 | 0.88 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1815 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 2Y08 · Structure of the substrate-free FAD-dependent tirandamycin oxidase TamL · the same entry in another collection · chain A against A, TM-score 1.00
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 D3Y1I2
- Elsewhere: RCSB PDB 2Y08 · PDBe 2Y08 · UniProt D3Y1I2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.