MolNFT v1 · #151292 · protein

Xray structure of glic in complex with crotonate

6HJI · Proton-gated ion channel: “Xray structure of glic in complex with crotonate”. X-ray diffraction, 4 ligands (PLC, BEO, NA), 20 pockets (best druggability 0.81). MolNFT v1 #151292 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6HJI
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, BEO, NA, CL
Pockets: 20 · best druggability 0.81

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 · 15 copies · chains A, B, C, D, E
BEO · Butenoic acid · ligand · 5 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 12 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1113	0.81	0.82	59	NA, LMT
2	411	0.72	0.83	45	empty
3	387	0.72	0.83	48	empty
4	365	0.72	0.84	47	empty
5	363	0.72	0.84	47	empty

Interfaces

5 interfaces between chains.

B–C · 2268 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 2260 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 2255 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2253 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2214 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6HJI · Xray structure of GLIC in complex with crotonate · 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 6HJI · PDBe 6HJI · UniProt Q7NDN8

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