MolNFT v1 · #103505 · protein

X-ray structure of the mouse serotonin 5-HT3 receptor

4PIR · 5-hydroxytryptamine receptor 3A: “X-ray structure of the mouse serotonin 5-HT3 receptor”. X-ray diffraction, 4 ligands (NAG, BMA, CL), 20 pockets (best druggability 0.83). MolNFT v1 #103505 on GenesisL1: 3D structure, binding sites…

PDB: 4PIR
Type: protein
Length: 2,535 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5-hydroxytryptamine receptor 3A; VHH15
UniProt: P23979
Ligands: NAG, BMA, CL, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	5-hydroxytryptamine receptor 3A	protein	383	40% helix, 25% strand	P23979
C, D	5-hydroxytryptamine receptor 3A	protein	384	40% helix, 26% strand	P23979
F	VHH15	protein	122	2% helix, 58% strand	—
G, H, I, J	VHH15	protein	124	2% helix, 59% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D, E
BMA · beta-D-mannopyranose · sugar · 5 copies
CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
SO4 · Sulfate ion · ion · 3 copies · chains B, C, D, E, H

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	900	0.83	0.84	82	empty
2	338	0.81	0.90	56	empty
3	802	0.80	0.83	77	empty
4	902	0.80	0.82	82	empty
5	894	0.80	0.82	76	empty

Interfaces

15 interfaces between chains.

B–C · 3191 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 3174 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 3165 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 3138 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 3137 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 glycan, 9 disulfide (N-glycosylation, disulfide).

Compared structures

4PIR · X-ray structure of the mouse serotonin 5-HT3 receptor · the same entry in another collection · chain J against J, TM-score 1.00
P23979 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 3A (P23979) · 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 P23979
Elsewhere: RCSB PDB 4PIR · PDBe 4PIR · UniProt P23979

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