MolNFT v1 · #98870 · protein

Glic liganded-closed-channel conformation, mutant Y27'A

4LMK · Proton-gated ion channel: “Glic liganded-closed-channel conformation, mutant Y27'A”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.81). MolNFT v1 #98870 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4LMK
Type: protein
Length: 1,550 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proton-gated ion channel
UniProt: Q7NDN8
Ligands: NA, CL
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, C, B, D	Proton-gated ion channel	protein	310	37% helix, 33% strand	Q7NDN8

Ligands and binding sites

NA · Sodium ion · metal · 5 copies · chains A, E, D, B, C
CL · Chloride ion · ion · 5 copies · chains A, E, C, B, D
LMT · Dodecyl-beta-D-maltoside · additive · chains A, E, C, B, 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	573	0.81	0.87	57	empty
2	571	0.81	0.87	54	empty
3	574	0.81	0.87	51	empty
4	580	0.80	0.85	57	empty
5	266	0.79	0.91	32	empty

Interfaces

10 interfaces between chains.

A–E · 2308 Å² buried · 19 hydrogen bonds · protein-protein
E–D · 2277 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 2251 Å² buried · 17 hydrogen bonds · protein-protein
C–B · 2247 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 2233 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4LMK · GLIC Liganded-closed-channel Conformation, Mutant Y27'A · the same entry in another collection · chain D against D, 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 0.97

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 4LMK · PDBe 4LMK · UniProt Q7NDN8

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