MolNFT v1 · #125750 · protein

X-ray structure of a pentameric ligand gated ion channel from erwinia chrysanthemi (elic) in complex with bromopromazine

5LID · Cys-loop ligand-gated ion channel: “X-ray structure of a pentameric ligand gated ion channel from erwinia chrysanthemi (elic) in complex with…”. X-ray diffraction, 1 ligand (6XY), 20 pockets (best druggability 0.84). MolNFT v1…

PDB: 5LID
Type: protein
Length: 3,070 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cys-loop ligand-gated ion channel
UniProt: P0C7B7
Ligands: 6XY
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Cys-loop ligand-gated ion channel	protein	307	32% helix, 29% strand	P0C7B7

Ligands and binding sites

6XY · bromopromazine · ion · 20 copies · chains A, B, C, D, E, F, G, H, I, J

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	860	0.84	0.86	80	6XY
2	1135	0.84	0.85	115	6XY
3	1086	0.83	0.84	89	6XY
4	986	0.83	0.84	94	6XY
5	927	0.83	0.84	89	6XY

Interfaces

15 interfaces between chains.

F–J · 2689 Å² buried · 21 hydrogen bonds · protein-protein
I–J · 2687 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 2667 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 2653 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2637 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5LID · X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC)… · the same entry in another collection · chain J against J, TM-score 1.00
P0C7B7 · AlphaFold monomer V2.0 prediction for cys-loop ligand-gated ion channel (P0C7B7) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P0C7B7
Elsewhere: RCSB PDB 5LID · PDBe 5LID · UniProt P0C7B7

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