5E94: Antibody Fab fragment light chain

Antibody-bound Glucagon-like Peptide-1 receptor extracellular domain. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Aug 2016.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 8,974
Mol. weight: 125.38 kDa
Released: 24 Aug 2016

Explore 5E94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E94 contains 48 α-helices and 108 β-strands across 6 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5
α-helix	211-213	3

Chain B: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	34-40	7	2
β-strand	46-53	8	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-101	10	2
β-strand	108-113	6	2
β-strand	117-119	3	2
β-strand	120-121	2	7
α-helix	124-126	3
β-strand	127	1	8
α-helix	128-129	2
β-strand	130-134	5	9
β-strand	145-155	11	9
β-strand	156	1	8
β-strand	161-164	4	10
α-helix	165-167	3
β-strand	169	1	10
β-strand	173-175	3	9
α-helix	176-178	3
β-strand	179-180	2	9
β-strand	186-195	10	9
α-helix	196-198	3
β-strand	199	1	11
β-strand	202	1	11
β-strand	205-210	6	10
α-helix	211-213	3
β-strand	215-220	6	10

Chain C: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	33-38	6	13
β-strand	44-49	6	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-106	5	13
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-154	2	16
α-helix	155	1
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-187	5
β-strand	191-197	7	16
β-strand	205-210	6	16
α-helix	211-213	3

Chain D: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
β-strand	34-41	8	19
β-strand	45-53	9	19
β-strand	58-60	3	19
β-strand	68-73	6	17
α-helix	74-76	3
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-102	11	19
β-strand	107-113	7	19
β-strand	117-119	3	19
β-strand	120-121	2	18
α-helix	125-126	2
β-strand	127	1	20
α-helix	128-129	2
β-strand	130-134	5	21
β-strand	145-155	11	21
β-strand	156	1	20
β-strand	161-164	4	22
α-helix	165-167	3
β-strand	169	1	22
β-strand	173-175	3	21
α-helix	176-178	3
β-strand	179-180	2	21
β-strand	186-195	10	21
β-strand	199	1	23
β-strand	202	1	23
β-strand	205-210	6	22
α-helix	211-213	3
β-strand	215-220	6	22

Chain G: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	32-52	21
α-helix	54-56	3
α-helix	61	1
β-strand	62	1	24
α-helix	63-64	2
β-strand	65-66	2	25
β-strand	71-72	2	25
β-strand	75	1	24
β-strand	79-84	6	26
α-helix	85-86	2
β-strand	99-104	6	26
α-helix	109	1
β-strand	110	1	26
α-helix	111	1
β-strand	122	1	26
α-helix	124-126	3
α-helix	137-142	6

Chain H: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	32-52	21
α-helix	54-56	3
β-strand	62	1	27
α-helix	63-64	2
β-strand	65-66	2	28
β-strand	71-72	2	28
β-strand	75	1	27
β-strand	79-84	6	29
α-helix	92-94	3
β-strand	99-104	6	29
β-strand	110	1	29
β-strand	122	1	29
α-helix	124-126	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody Fab fragment light chain	A, C	protein	214	Mus musculus
Antibody Fab fragment heavy chain	B, D	protein	224	Mus musculus
Glucagon-like peptide 1 receptor	G, H	protein	126	Homo sapiens	P43220 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5E94_1 Antibody Fab fragment light chain (chains A, C)
DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISSLEQEDVATYFCQQGNTLPFTFGSGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>5E94_2 Antibody Fab fragment heavy chain (chains B, D)
DVQLQESGPGLVKPSQSLSLTCTVTGYSITSTYDWHWIRHFPGNILEWMGYISYSGSTNY
NPSLKSRISITHDTSKNRFFLKLNSVTSEDTATYYCARATASFYDGSYYFDYWGQGTTLT
VSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESK

Sequence of entity 3 (G, H), FASTA

>5E94_3 Glucagon-like peptide 1 receptor (chains G, H)
GSHMRPQGATVSLWETVQKWREYRRQCQRSLTEDPPPATDLFCNRTFDEYACWPDGEPGS
FVNVSCPWYLPWASSVPQGHVYRFCTAEGLWLQKDNSSLPWRDLSECEESKRGERSSPEE
QLLFLY

Primary citation

Structural insight into antibody-mediated antagonism of the Glucagon-like peptide-1 Receptor. Hennen, S., Kodra, J.T., Soroka, V. et al. Sci Rep (2016) 6:26236-26236. DOI 10.1038/srep26236 · PubMed

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

4ZGM 1.8 Å, Crystal structure of Semaglutide peptide backbone in complex with the GLP-1 receptor…
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
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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