MolNFT v1 · #118729 · protein

Wild-type choline tma lyase in complex with choline

5FAU · Choline trimethylamine-lyase: “Wild-type choline tma lyase in complex with choline”. X-ray diffraction, 1 ligand (CHT), 20 pockets (best druggability 0.82). MolNFT v1 #118729 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5FAU
Type: protein
Length: 3,179 residues
Chains: 4
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
Pockets: 20 · best druggability 0.82

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	794	52% helix, 9% strand	Q30W70
B, C, D	Choline trimethylamine-lyase (EC 4.3.99.4)	protein	795	52% helix, 9% strand	Q30W70

Ligands and binding sites

CHT · Choline ion · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 8 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	954	0.82	0.83	68	empty
2	1047	0.82	0.83	74	empty
3	194	0.78	0.93	31	empty
4	147	0.77	0.95	23	empty
5	188	0.76	0.92	27	empty

Interfaces

4 interfaces between chains.

B–D · 1521 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1471 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 1034 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1030 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5FAU · wild-type choline TMA lyase in complex with choline · the same entry in another collection · chain D against D, 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 5FAU · PDBe 5FAU · UniProt Q30W70

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.