4ZGM: Semaglutide peptide backbone

Crystal structure of Semaglutide peptide backbone in complex with the GLP-1 receptor extracellular domain. Determined by X-ray diffraction at 1.8 Å resolution. Released 9 Sept 2015.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,195
Mol. weight: 18.52 kDa
Ligands: 32M
Released: 9 Sept 2015

Explore 4ZGM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZGM contains 9 α-helices and 10 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	32-52	21
α-helix	54-56	3
β-strand	62	1	1
α-helix	63	1
β-strand	65-66	2	2
β-strand	71-72	2	2
α-helix	73-74	2
β-strand	75	1	1
β-strand	79-84	6	3
α-helix	85-86	2
α-helix	92-94	3
β-strand	99-104	6	3
β-strand	110	1	3
β-strand	112	1	4
β-strand	119	1	4
α-helix	120	1
β-strand	122	1	3
α-helix	124-126	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-33	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glucagon-like peptide 1 receptor	A	protein	122	Homo sapiens	P43220 (AlphaFold model)
Semaglutide peptide backbone; 8Aib,34R-GLP-1(7-37)-OH	B	protein	31	Homo sapiens	P01275 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4ZGM_1 Glucagon-like peptide 1 receptor (chains A)
RPQGATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGSFVNV
SCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEESKRGERSSPEEQLLF
LY

Sequence of entity 2 (B), FASTA

>4ZGM_2 Semaglutide peptide backbone; 8Aib,34R-GLP-1(7-37)-OH (chains B)
HAEGTFTSDVSSYLEGQAAKEFIAWLVRGRG

Ligands and cofactors

ID	Name	Formula	Copies
32M	3,6,9,12,15,18-hexaoxahexacosan-1-ol	C20 H42 O7	2

Primary citation

Discovery of the Once-Weekly Glucagon-Like Peptide-1 (GLP-1) Analogue Semaglutide. Lau, J., Bloch, P., Schaffer, L. et al. J Med Chem (2015) 58:7370-7380. DOI 10.1021/acs.jmedchem.5b00726 · PubMed

Other PDB entries of the same protein (UniProt P43220 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5OTU 1.8 Å, Extracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Hcs/Thr11Hcs
5OTT 1.92 Å, Extracellular domain of GLP-1 receptor in complex with exendin-4 variant Gly2Hcs/Thr5Hcs
5E94 2.0 Å, Antibody-bound Glucagon-like Peptide-1 receptor extracellular domain
5OTV 2.0 Å, Extracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Cyc/Thr11Hcs
5OTX 2.0 Å, Extracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Cys/Thr11Cys
3C5T 2.1 Å, Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular…
3IOL 2.1 Å, Crystal structure of Glucagon-Like Peptide-1 in complex with the extracellular domain of…
5OTW 2.1 Å, Extracellular domain of GLP-1 receptor in complex with GLP-1 variant Ala8Hcs/Thr11Cys
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

Browse structure collections

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