Research workbench
Y208F mutant of choline tma-lyase
Analyse Y208F mutant of choline tma-lyase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FAY
- Type
- protein
- Length
- 1,583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline trimethylamine-lyase
- EC
- 4.3.99.4
- UniProt
- Q30W70
- Ligands
- CHT, NA
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline trimethylamine-lyase (EC 4.3.99.4) | protein | 803 | 52% helix, 9% strand | Q30W70 |
| B | Choline trimethylamine-lyase (EC 4.3.99.4) | protein | 780 | 51% helix, 9% strand | Q30W70 |
Ligands and binding sites
- CHT · Choline ion · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- MLI · Malonate ion · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.84 | 0.91 | 59 | NA |
| 2 | 299 | 0.62 | 0.80 | 30 | MLI |
| 3 | 200 | 0.60 | 0.82 | 32 | empty |
| 4 | 204 | 0.56 | 0.79 | 28 | empty |
| 5 | 155 | 0.47 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1146 Ų buried · 17 hydrogen bonds · protein-protein
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 Q30W70
- Elsewhere: RCSB PDB 5FAY · PDBe 5FAY · UniProt Q30W70
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