MolNFT v1 · #178310 · protein

Structure of a channel

7FBS · Sodium channel protein type 5 subunit ALPHA,SODIUM channel…: “Structure of a channel”. Electron microscopy, 4 ligands (6OU, 9Z9, 4Y4), 20 pockets (best druggability 0.83). MolNFT v1 #178310 on GenesisL1: 3D structure, binding sites…

PDB: 7FBS
Type: protein
Length: 1,118 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sodium channel protein type 5 subunit ALPHA,SODIUM channel protein type 5 subunit…
UniProt: P15389
Ligands: 6OU, 9Z9, 4Y4, NAG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 70% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sodium channel protein type 5 subunit ALPHA,SODIUM channel protein type 5 subunit ALPHA,SODIUM channel protein type 5 subunit ALPHA,G PROTEIN/GFP fusion protein	protein	1118	70% helix, 1% strand	P15389

Ligands and binding sites

6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 11 copies · chains A
9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · 2 copies · chains A
4Y4 · 1-[2-[(2R)-2-oxidanyl-3-(propylamino)propoxy]phenyl]-3-phenyl-propan-1-one · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	797	0.83	0.85	89	4Y4, 6OU, 9Z9
2	487	0.69	0.80	56	empty
3	214	0.62	0.81	17	9Z9
4	330	0.60	0.77	46	empty
5	154	0.59	0.83	29	empty

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7FBS · structure of a channel · the same entry in another collection · chain A against A, TM-score 1.00
P15389 · AlphaFold monomer V2.0 prediction for sodium channel protein type 5 subunit alpha (P15389) · 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 P15389
Elsewhere: RCSB PDB 7FBS · PDBe 7FBS · UniProt P15389

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