MolNFT v1 · #122821 · protein

Crystal structure of glic in complex with dha

5J0Z · Proton-gated ion channel: “Crystal structure of glic in complex with dha”. X-ray diffraction, 4 ligands (HXA, PLC, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #122821 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5J0Z
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: HXA, PLC, SO4, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	36% helix, 33% strand	Q7NDN8

Ligands and binding sites

HXA · Docosa-4,7,10,13,16,19-hexaenoic acid · ligand · 5 copies · chains A, E, B, C, D
PLC · Diundecyl phosphatidyl choline · ligand · chains A
SO4 · Sulfate ion · ion · 6 copies · chains A, E, B, C, D
CL · Chloride ion · ion · 3 copies · chains A, D, E
LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, D, E, B, C
ACT · Acetate ion · additive · 2 copies · chains A, E, 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	1121	0.81	0.82	63	LMT
2	59	0.70	0.97	20	empty
3	54	0.69	0.97	18	empty
4	55	0.68	0.96	20	empty
5	55	0.67	0.96	19	empty

Interfaces

5 interfaces between chains.

B–C · 2379 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 2370 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 2349 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2349 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 2311 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5J0Z · Crystal structure of GLIC in complex with DHA · 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 0.99

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 5J0Z · PDBe 5J0Z · UniProt Q7NDN8

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