MolNFT v1 · #151861 · protein

The glic pentameric ligand-gated ion channel mutant E243C-I201W

6I08 · Proton-gated ion channel: “The glic pentameric ligand-gated ion channel mutant E243C-I201W”. X-ray diffraction, 3 ligands (PLC, NA, CL), 20 pockets (best druggability 0.90). MolNFT v1 #151861 on GenesisL1: 3D structure, binding…

PDB: 6I08
Type: protein
Length: 1,555 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: PLC, NA, CL
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C, E	Proton-gated ion channel	protein	311	36% helix, 33% strand	Q7NDN8

Ligands and binding sites

PLC · Diundecyl phosphatidyl choline · ligand · 5 copies · chains D, A, B, C, E
NA · Sodium ion · metal · 7 copies · chains D, A, B, E, C
CL · Chloride ion · ion · 5 copies · chains D, A, B, C, E
LMT · Dodecyl-beta-D-maltoside · additive · chains D, A, B, C, E

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1124	0.90	0.91	116	empty
2	446	0.84	0.91	54	LMT, NA
3	271	0.80	0.92	31	empty
4	565	0.75	0.83	69	CL, NA
5	556	0.75	0.82	58	CL, NA

Interfaces

5 interfaces between chains.

A–B · 2330 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 2313 Å² buried · 16 hydrogen bonds · protein-protein
D–C · 2275 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 2274 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 2266 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6I08 · The glic pentameric ligand-gated ion channel mutant E243C-I201W · the same entry in another collection · chain E against E, TM-score 1.00
Q7NDN8 · AlphaFold monomer V2.0 prediction for proton-gated ion channel (Q7NDN8) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 Q7NDN8
Elsewhere: RCSB PDB 6I08 · PDBe 6I08 · UniProt Q7NDN8

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