Research workbench

Glic mutant D86A

Analyse Glic mutant D86A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F11
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 0.81

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 · 2 copies · chains B, C
NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 7 copies · chains A, B, C, D, E
ACT · Acetate ion · additive · 10 copies · chains A, B, C, D, E
LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, E, 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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1135	0.81	0.82	60	LMT, NA
2	375	0.71	0.83	45	empty
3	393	0.70	0.82	46	empty
4	349	0.70	0.83	49	empty
5	566	0.70	0.79	66	CL, NA, ACT

Interfaces

5 interfaces between chains.

A–B · 2250 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 2244 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 2233 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 2218 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 2215 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6F11 · GLIC mutant D86A · 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 6F11 · PDBe 6F11 · UniProt Q7NDN8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.