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A molecular basis for negative regulation of the glucagon receptor

Analyse A molecular basis for negative regulation of the glucagon receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ERS
Type: protein
Length: 541 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain; Glucagon receptor
UniProt: P47871
Ligands: NAG
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	214	4% helix, 48% strand	—
H	Fab heavy chain	protein	231	9% helix, 52% strand	—
A	Glucagon receptor	protein	96	20% helix, 25% strand	P47871

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, L

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	377	0.58	0.76	61	empty
2	120	0.54	0.83	31	empty
3	71	0.38	0.78	20	empty
4	51	0.31	0.77	11	empty
5	67	0.29	0.73	16	empty

Interfaces

2 interfaces between chains.

L–H · 1844 Å² buried · 13 hydrogen bonds · protein-protein
L–A · 274 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4ERS · A Molecular Basis for Negative Regulation of the Glucagon 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 A against A, TM-score 0.96

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
Elsewhere: RCSB PDB 4ERS · PDBe 4ERS · UniProt P47871

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