Research workbench
E491A mutant of choline tma-lyase
Analyse E491A 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
- 5KDP
- Type
- protein
- Length
- 1,609 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
- NA
- Pockets
- 14 · best druggability 0.83
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 |
| C | Choline trimethylamine-lyase (EC 4.3.99.4) | protein | 806 | 51% helix, 9% strand | Q30W70 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- MLI · Malonate ion · additive · 6 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.83 | 0.92 | 58 | NA |
| 2 | 197 | 0.65 | 0.84 | 36 | empty |
| 3 | 227 | 0.63 | 0.82 | 36 | empty |
| 4 | 258 | 0.61 | 0.80 | 26 | MLI |
| 5 | 175 | 0.50 | 0.78 | 38 | empty |
Interfaces
1 interface between chains.
- A–C · 1118 Ų buried · 16 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 5KDP · PDBe 5KDP · UniProt Q30W70
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