MolNFT v1 · #104779 · protein

Structure of BETA2 adrenoceptor bound to a covalent agonist and an engineered nanobody

4QKX · Beta-2 adrenergic receptor: “Structure of BETA2 adrenoceptor bound to a covalent agonist and an engineered nanobody”. X-ray diffraction, 2 ligands (35V, NA), 6 pockets (best druggability 0.80). MolNFT v1 #104779 on GenesisL1: 3D…

PDB: 4QKX
Type: protein
Length: 574 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-2 adrenergic receptor; R9 protein
EC: 3.2.1.17
UniProt: D9IEF7, P07550
Ligands: 35V, NA
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-2 adrenergic receptor (EC 3.2.1.17)	protein	454	71% helix, 3% strand	D9IEF7, P07550
B	R9 protein	protein	120	3% helix, 54% strand	—

Ligands and binding sites

35V · 4-[(1R)-1-hydroxy-2-({2-[3-methoxy-4-(2-sulfanylethoxy)phenyl]ethyl}amino)ethyl]benzene-1,2-diol · ligand · chains A
NA · Sodium ion · metal · 2 copies · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1144	0.80	0.81	102	35V
2	336	0.62	0.78	39	empty
3	106	0.42	0.77	26	empty
4	90	0.40	0.77	19	empty
5	67	0.32	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 1166 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

4QKX · Structure of beta2 adrenoceptor bound to a covalent agonist and an engineered nanobody · the same entry in another collection · chain A against A, TM-score 1.00
P07550 · AlphaFold monomer V2.0 prediction for beta-2 adrenergic receptor (P07550) · a predicted model of the same protein · chain A against A, TM-score 0.61

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 D9IEF7
Every structure of UniProt P07550
Elsewhere: RCSB PDB 4QKX · PDBe 4QKX · UniProt D9IEF7 · UniProt P07550

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.