MolNFT v1 · #139413 · protein

Structure of the full-length glucagon class B G protein-coupled receptor

5XEZ · Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor: “Structure of the full-length glucagon class B G protein-coupled receptor”. X-ray diffraction, 2 ligands (97V, NAG), 19 pockets (best druggability 0.78). MolNFT v1 #139413 on GenesisL1…

PDB: 5XEZ
Type: protein
Length: 1,934 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor; Antibody, MAB1, heavy chain; Antibody…
EC: 3.2.1.17
UniProt: P47871, D9IEF7
Ligands: 97V, NAG
Pockets: 19 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor (EC 3.2.1.17)	protein	545	59% helix, 8% strand	P47871, D9IEF7
B	Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor (EC 3.2.1.17)	protein	499	62% helix, 7% strand	P47871, D9IEF7
C, H	Antibody, MAB1, heavy chain	protein	231	9% helix, 55% strand	—
D, L	Antibody, MAB1, light chain	protein	214	7% helix, 49% strand	—

Ligands and binding sites

97V · 4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl) phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl) benzamide · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, D

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

Pockets

19 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	617	0.78	0.83	49	empty
2	979	0.74	0.77	75	empty
3	659	0.69	0.77	73	empty
4	428	0.67	0.79	56	empty
5	339	0.64	0.80	45	empty

Interfaces

10 interfaces between chains.

C–D · 1993 Å² buried · 20 hydrogen bonds · protein-protein
H–L · 1974 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 969 Å² buried · 13 hydrogen bonds · protein-protein
B–H · 958 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 795 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

5XEZ · Structure of the Full-length glucagon class B G protein-coupled receptor · the same entry in another collection · chain L against L, TM-score 1.00
P47871 · AlphaFold monomer V2.0 prediction for glucagon receptor (P47871) · a predicted model of the same protein · chain B against A, TM-score 0.51

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 P47871
Every structure of UniProt D9IEF7
Elsewhere: RCSB PDB 5XEZ · PDBe 5XEZ · UniProt P47871 · UniProt D9IEF7

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