MolNFT v1 · #151308 · protein

Xray structure of glic in complex with succinate

6HJZ · Proton-gated ion channel: “Xray structure of glic in complex with succinate”. X-ray diffraction, 3 ligands (PLC, NA, CL), 20 pockets (best druggability 0.82). MolNFT v1 #151308 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6HJZ
Type: protein
Length: 3,110 residues
Chains: 10
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 0.82

Structure

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

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

Ligands and binding sites

PLC · Diundecyl phosphatidyl choline · ligand · 30 copies · chains A, B, C, D, E, F, G, H, I, J
NA · Sodium ion · metal · 12 copies · chains A, B, C, E, D, F, G, H, J, I
CL · Chloride ion · ion · 14 copies · chains A, B, C, D, E, F, G, H, I, J
SIN · Succinic acid · additive · 20 copies · chains A, E, B, C, D, F, J, G, H, I
LMT · Dodecyl-beta-D-maltoside · additive · 12 copies · chains A, B, E, C, D, F, G, J, H, I

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	1126	0.82	0.82	63	LMT, NA
2	1085	0.82	0.82	60	LMT, NA
3	454	0.75	0.84	62	empty
4	424	0.72	0.83	47	empty
5	374	0.72	0.83	48	empty

Interfaces

15 interfaces between chains.

A–B · 2326 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 2308 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 2303 Å² buried · 16 hydrogen bonds · protein-protein
H–I · 2296 Å² buried · 12 hydrogen bonds · protein-protein
F–J · 2284 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6HJZ · Xray structure of GLIC in complex with succinate · the same entry in another collection · chain J against J, 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 6HJZ · PDBe 6HJZ · UniProt Q7NDN8

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