MolNFT v1 · #151285 · protein

Xray structure of glic in complex with malonate

6HJB · Proton-gated ion channel: “Xray structure of glic in complex with malonate”. X-ray diffraction, 3 ligands (PLC, NA, CL), 20 pockets (best druggability 0.81). MolNFT v1 #151285 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6HJB
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, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Proton-gated ion channel	protein	311	37% helix, 35% strand	Q7NDN8

Ligands and binding sites

PLC · Diundecyl phosphatidyl choline · ligand · 11 copies · chains A, B, C, D, E
NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E
CL · Chloride ion · ion · 11 copies · chains A, B, C, D, E
LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, E, C, D
MLA · Malonic acid · additive · 5 copies · chains A, E, B, 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	1135	0.81	0.82	58	LMT
2	399	0.73	0.83	46	empty
3	365	0.72	0.84	48	empty
4	434	0.72	0.82	48	empty
5	401	0.72	0.83	49	empty

Interfaces

5 interfaces between chains.

C–D · 2298 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 2287 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 2273 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 2263 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 2254 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6HJB · Xray structure of GLIC in complex with malonate · 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 D 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 6HJB · PDBe 6HJB · UniProt Q7NDN8

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