Research workbench
Wild-type choline tma lyase in complex with 1-methyl-1,2,3,6- tetrahydropyridin-3-ol
Analyse Wild-type choline tma lyase in complex with 1-methyl-1,2,3,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VUE
- Type
- protein
- Length
- 1,604 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
- RP7, NA
- Pockets
- 18 · best druggability 0.78
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 | 801 | 53% helix, 9% strand | Q30W70 |
Ligands and binding sites
- RP7 · (3S)-1-methyl-1,2,3,6-tetrahydropyridin-3-ol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.78 | 0.93 | 27 | NA |
| 2 | 235 | 0.74 | 0.89 | 29 | NA |
| 3 | 292 | 0.63 | 0.80 | 28 | empty |
| 4 | 194 | 0.62 | 0.83 | 35 | empty |
| 5 | 197 | 0.60 | 0.82 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 1062 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6VUE · wild-type choline TMA lyase in complex with 1-methyl-1,2,3,6-tetrahydropyridin-3-ol · the same entry in another collection · chain A against A, TM-score 1.00
- Q30W70 · AlphaFold monomer V2.0 prediction for choline trimethylamine-lyase (Q30W70) · a predicted model of the same protein · chain B 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 Q30W70
- Elsewhere: RCSB PDB 6VUE · PDBe 6VUE · UniProt Q30W70
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