MolNFT v1 · #146515 · protein
Structure of TYW1 with a lysine-pyruvate adduct bound
6DJT · S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine…: “Structure of TYW1 with a lysine-pyruvate adduct bound”. X-ray diffraction, 2 ligands (SF4, FS0), 1 pocket (best druggability 0.76). MolNFT v1 #146515 on GenesisL1: 3D…
- PDB
- 6DJT
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase
- EC
- 4.1.3.44
- UniProt
- Q57705
- Ligands
- SF4, FS0
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase (EC 4.1.3.44) | protein | 298 | 44% helix, 17% strand | Q57705 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- FS0 · Fe2/s3 cluster · ligand · chains A
- GOL · Glycerol · additive · 8 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.76 | 0.79 | 70 | SF4, GOL, FS0 |
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
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 Q57705
- Elsewhere: RCSB PDB 6DJT · PDBe 6DJT · UniProt Q57705
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