MolNFT v1 · #157866 · protein
Wild-type choline tma lyase in complex with betaine aldehyde
6ND3 · Choline trimethylamine-lyase: “Wild-type choline tma lyase in complex with betaine aldehyde”. X-ray diffraction, 1 ligand (BTL), 20 pockets (best druggability 0.83). MolNFT v1 #157866 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ND3
- Type
- protein
- Length
- 6,360 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline trimethylamine-lyase
- EC
- 4.3.99.4
- UniProt
- Q30W70
- Ligands
- BTL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Choline trimethylamine-lyase (EC 4.3.99.4) | protein | 795 | 52% helix, 9% strand | Q30W70 |
| B, F | Choline trimethylamine-lyase (EC 4.3.99.4) | protein | 794 | 52% helix, 9% strand | Q30W70 |
| D, H | Choline trimethylamine-lyase (EC 4.3.99.4) | protein | 796 | 50% helix, 9% strand | Q30W70 |
Ligands and binding sites
- BTL · Betaine aldehyde · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.83 | 0.91 | 58 | empty |
| 2 | 964 | 0.83 | 0.84 | 70 | empty |
| 3 | 943 | 0.82 | 0.83 | 67 | empty |
| 4 | 1045 | 0.82 | 0.83 | 71 | empty |
| 5 | 1090 | 0.81 | 0.82 | 75 | empty |
Interfaces
10 interfaces between chains.
- E–G · 1522 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1522 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1521 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1480 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1049 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6ND3 · wild-type choline TMA lyase in complex with betaine aldehyde · the same entry in another collection · chain H against H, TM-score 1.00
- Q30W70 · AlphaFold monomer V2.0 prediction for choline trimethylamine-lyase (Q30W70) · a predicted model of the same protein · chain G 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 6ND3 · PDBe 6ND3 · UniProt Q30W70
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