MolNFT v1 · #151814 · protein

The glic pentameric ligand-gated ion channel mutant Y119A

6HYV · Proton-gated ion channel: “The glic pentameric ligand-gated ion channel mutant Y119A”. X-ray diffraction, 3 ligands (PLC, NA, CL), 20 pockets (best druggability 0.82). MolNFT v1 #151814 on GenesisL1: 3D structure, binding sites and…

PDB: 6HYV
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 0.82

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	37% helix, 33% strand	Q7NDN8

Ligands and binding sites

PLC · Diundecyl phosphatidyl choline · ligand · 10 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E
LMT · Dodecyl-beta-D-maltoside · additive · 11 copies · chains A, B, E, C, D
ACT · Acetate ion · additive · 10 copies · chains A, E, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1165	0.82	0.82	62	NA, LMT
2	485	0.75	0.83	47	LMT
3	527	0.74	0.82	50	LMT
4	480	0.73	0.82	50	LMT
5	491	0.73	0.82	49	LMT

Interfaces

5 interfaces between chains.

A–B · 2270 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 2253 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 2244 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 2233 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 2225 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6HYV · The glic pentameric ligand-gated ion channel mutant Y119A · 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 A 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 Q7NDN8
Elsewhere: RCSB PDB 6HYV · PDBe 6HYV · UniProt Q7NDN8

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