Research workbench

Xray structure of glic in complex with glutarate

Analyse Xray structure of glic in complex with glutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HJA
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, D12, GUA, NA, CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	37% helix, 34% strand	Q7NDN8

Ligands and binding sites

PLC · Diundecyl phosphatidyl choline · ligand · 14 copies · chains A, B, C, D, E
D12 · Dodecane · ligand · 6 copies · chains A, E, B, C, D
GUA · Glutaric acid · ligand · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 4 copies · chains B, A, C, D, E
CL · Chloride ion · ion · 11 copies · 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, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1174	0.82	0.82	63	D12, NA
2	491	0.76	0.84	61	empty
3	428	0.73	0.83	54	empty
4	409	0.73	0.83	50	empty
5	379	0.72	0.83	50	empty

Interfaces

5 interfaces between chains.

B–C · 2318 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 2267 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 2264 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2258 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 2249 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6HJA · Xray structure of GLIC in complex with glutarate · 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 6HJA · PDBe 6HJA · UniProt Q7NDN8

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