MolNFT v1 · #120825 · protein

Cationic ligand-gated ion channel

5HCJ · Proton-gated ion channel: “Cationic ligand-gated ion channel”. X-ray diffraction, 3 ligands (MBR, NA, CL), 20 pockets (best druggability 0.85). MolNFT v1 #120825 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HCJ
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: MBR, NA, CL
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	36% helix, 34% strand	Q7NDN8

Ligands and binding sites

MBR · Tribromomethane · ligand · chains A, B, C, D, E
NA · Sodium ion · metal · chains A, B
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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.85	0.88	97	empty
2	329	0.85	0.95	38	LMT, NA, MBR
3	535	0.83	0.89	73	empty
4	375	0.80	0.89	51	empty
5	257	0.74	0.88	34	empty

Interfaces

7 interfaces between chains.

A–B · 2281 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 2273 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 2257 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 2250 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 2248 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5HCJ · Cationic Ligand-Gated Ion Channel · 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 0.98

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 5HCJ · PDBe 5HCJ · UniProt Q7NDN8

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