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5-HT3A receptor in salipro (apo, asymmetric)

Analyse 5-HT3A receptor in salipro (apo, asymmetric) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y5B
Type: protein
Length: 1,887 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5-hydroxytryptamine receptor 3A
UniProt: P23979
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 5 distinct chains · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5-hydroxytryptamine receptor 3A	protein	378	42% helix, 24% strand	P23979
B	5-hydroxytryptamine receptor 3A	protein	375	42% helix, 25% strand	P23979
C	5-hydroxytryptamine receptor 3A	protein	378	44% helix, 25% strand	P23979
D	5-hydroxytryptamine receptor 3A	protein	377	41% helix, 23% strand	P23979
E	5-hydroxytryptamine receptor 3A	protein	379	42% helix, 22% strand	P23979

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	0.87	0.88	105	empty
2	181	0.79	0.94	34	empty
3	279	0.73	0.86	34	empty
4	59	0.71	0.97	21	empty
5	496	0.70	0.80	39	empty

Interfaces

6 interfaces between chains.

C–D · 3075 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 2916 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2907 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 2609 Å² buried · 21 hydrogen bonds · protein-protein
A–E · 2482 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

6Y5B · 5-HT3A receptor in Salipro (apo, asymmetric) · the same entry in another collection · chain E against E, TM-score 1.00
P23979 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 3A (P23979) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P23979
Elsewhere: RCSB PDB 6Y5B · PDBe 6Y5B · UniProt P23979

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