MolNFT v1 · #151792 · protein

The glic pentameric ligand-gated ion channel mutant Q193M

6HY9 · Proton-gated ion channel: “The glic pentameric ligand-gated ion channel mutant Q193M”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.82). MolNFT v1 #151792 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6HY9
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: CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	35% helix, 33% strand	Q7NDN8

Ligands and binding sites

CL · Chloride ion · ion · 5 copies · chains A, E, B, C, D
LMT · Dodecyl-beta-D-maltoside · additive · chains A, B, C, D, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1030	0.82	0.83	91	empty
2	617	0.81	0.86	54	LMT
3	145	0.80	0.97	26	empty
4	142	0.80	0.97	23	empty
5	151	0.80	0.96	24	empty

Interfaces

5 interfaces between chains.

C–D · 2284 Å² buried · 25 hydrogen bonds · protein-protein
A–E · 2232 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 2230 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2216 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 2184 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6HY9 · The glic pentameric ligand-gated ion channel mutant Q193M · 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 B against A, TM-score 0.97

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 6HY9 · PDBe 6HY9 · UniProt Q7NDN8

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