MolNFT v1 · #54911 · protein
Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase taml in C2 space group
2Y3S: “Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase taml in C2 space group”. X-ray diffraction, 4 ligands (FAD, TIR, MG), 10 pockets (best druggability 0.89). MolNFT v1 #54911 on GenesisL1: 3D structure, binding…
- PDB
- 2Y3S
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Taml
- UniProt
- D3Y1I2
- Ligands
- FAD, TIR, MG, CL
- Pockets
- 10 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taml | protein | 497 | 31% helix, 22% strand | D3Y1I2 |
| B | Taml | protein | 493 | 32% helix, 22% strand | D3Y1I2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TIR · Tirandamycin E · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 5 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.89 | 0.93 | 153 | FAD, TIR, GOL |
| 2 | 413 | 0.85 | 0.93 | 71 | FAD, TIR |
| 3 | 51 | 0.53 | 0.89 | 14 | empty |
| 4 | 137 | 0.47 | 0.78 | 21 | empty |
| 5 | 65 | 0.42 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1895 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 2Y3S · Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase TamL in C2 space… · 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 2Y3S · PDBe 2Y3S · UniProt D3Y1I2
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