MolNFT v1 · #151816 · protein

The glic pentameric ligand-gated ion channel mutant Y197F-P250C

6HYX · Proton-gated ion channel: “The glic pentameric ligand-gated ion channel mutant Y197F-P250C”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.85). MolNFT v1 #151816 on GenesisL1: 3D structure, binding sites and…

PDB: 6HYX
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: NA, CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	39% helix, 33% strand	Q7NDN8

Ligands and binding sites

NA · Sodium ion · metal · 7 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.85	0.86	108	LMT, NA
2	624	0.80	0.85	61	empty
3	643	0.79	0.84	67	empty
4	673	0.79	0.83	63	empty
5	696	0.78	0.83	60	empty

Interfaces

5 interfaces between chains.

B–C · 2239 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2236 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 2231 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 2201 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 2169 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6HYX · The glic pentameric ligand-gated ion channel mutant Y197F-P250C · 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 C against A, TM-score 0.98

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 6HYX · PDBe 6HYX · UniProt Q7NDN8

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