4LF3: Fab heavy chain

Inhibitory Mechanism of an Allosteric Antibody Targeting the Glucagon Receptor. Determined by X-ray diffraction at 2.73 Å resolution. Released 13 Nov 2013.

Method: X-ray diffraction
Resolution: 2.73 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 8,470
Mol. weight: 119.23 kDa
Released: 13 Nov 2013

Explore 4LF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LF3 contains 43 α-helices and 109 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	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	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	85-90	6	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	183-188	6
β-strand	191-197	7	5
α-helix	204	1
β-strand	205-210	6	5

Chain B: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	6
β-strand	224-226	3	7
β-strand	232-239	8	6
α-helix	243-245	3
β-strand	247-253	7	7
β-strand	260-265	6	7
β-strand	273-274	2	7
α-helix	276-278	3
β-strand	282-287	6	6
α-helix	288-290	3
β-strand	292-297	6	6
α-helix	302-304	3
β-strand	306-317	12	7
β-strand	324-332	9	7
β-strand	333	1	6
β-strand	336-340	5	7
α-helix	343-345	3
β-strand	346	1	8
α-helix	347-348	2
β-strand	349-353	5	9
β-strand	364-374	11	9
β-strand	375	1	8
β-strand	380-383	4	10
α-helix	384-386	3
β-strand	392-394	3	9
α-helix	395-397	3
β-strand	398-399	2	9
β-strand	405-414	10	9
α-helix	415-417	3
β-strand	418	1	11
β-strand	421	1	11
β-strand	423-429	7	10
α-helix	430-432	3
β-strand	434-440	7	10

Chain C: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	30-46	17
α-helix	51-53	3
β-strand	57-58	2	12
β-strand	61-62	2	13
β-strand	67-68	2	13
β-strand	71-72	2	12
β-strand	75-80	6	14
α-helix	81-82	2
β-strand	95-100	6	14
β-strand	106	1	14
β-strand	108	1	15
β-strand	114	1	15
β-strand	117	1	14
α-helix	119-121	3

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	85-90	6	17
β-strand	97-98	2	17
β-strand	102-106	5	17
α-helix	107	1
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	144-150	7	20
β-strand	153-154	2	20
β-strand	159-163	5	19
β-strand	173-182	10	19
α-helix	183-188	6
β-strand	191-198	8	20
β-strand	205-210	6	20

Chain E: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	21
β-strand	224-226	3	22
β-strand	232-239	8	21
β-strand	247-253	7	22
β-strand	259-265	7	22
β-strand	273-274	2	22
α-helix	276-278	3
β-strand	282-287	6	21
β-strand	292-297	6	21
α-helix	302-304	3
β-strand	306-317	12	22
β-strand	324-332	9	22
β-strand	336-340	5	22
β-strand	346	1	23
α-helix	347-348	2
β-strand	349-353	5	24
β-strand	364-374	11	24
β-strand	375	1	23
β-strand	380-383	4	25
α-helix	384-386	3
β-strand	393-394	2	24
α-helix	395-397	3
β-strand	398-399	2	24
β-strand	405-414	10	24
α-helix	415-417	3
β-strand	418	1	26
β-strand	421	1	26
β-strand	423-429	7	25
β-strand	434-440	7	25

Chain F: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	31-48	18
α-helix	51-53	3
β-strand	57-58	2	27
α-helix	59-60	2
β-strand	61-62	2	28
β-strand	67-68	2	28
β-strand	71-72	2	27
β-strand	75-80	6	29
α-helix	81-82	2
α-helix	88-91	4
β-strand	95-100	6	29
α-helix	101	1
β-strand	106	1	29
β-strand	108	1	30
β-strand	114	1	30
β-strand	117	1	29
α-helix	119-121	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab heavy chain	A, D	protein	214	Mus musculus
Fab light chain	B, E	protein	231	Mus musculus
Glucagon receptor	C, F	protein	95	Homo sapiens	P47871 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4LF3_1 Fab heavy chain (chains A, D)
DIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLESGVPS
RFSGSGSGTEFTLTISSVQPEDFVTYYCLQHNSNPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, E), FASTA

>4LF3_2 Fab light chain (chains B, E)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVMWYDGSNKDY
VDSVKGRFTISRDNSKNTLYLQMNRLRAEDTAVYYCAREKDHYDILTGYNYYYGLDVWGQ
GTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (C, F), FASTA

>4LF3_3 Glucagon receptor (chains C, F)
MDFLFEKWKLYSDQCHHNLSLLPPPTELVCNRTFDKYSCWPDTPANTTANISCPWYLPWH
HKVQHRFVFKRCGPDGQWVRGPRGQPWRDASQCQM

Primary citation

Inhibitory mechanism of an allosteric antibody targeting the glucagon receptor. Mukund, S., Shang, Y., Clarke, H.J. et al. J Biol Chem (2013) 288:36168-36178. DOI 10.1074/jbc.M113.496984 · PubMed

Other PDB entries of the same protein (UniProt P47871 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
2A83 1.4 Å, Crystal structure of hla-b*2705 complexed with the glucagon receptor (gr) peptide…
9N04 2.3 Å, Cryo-EM structure of GCGR-Gs complex with peptide 15
9N0E 2.3 Å, Cryo-EM structure of GCGR-Gs complex with oxyntomodulin
5EE7 2.5 Å, Crystal structure of the human glucagon receptor (GCGR) in complex with the antagonist…
9XN4 2.53 Å, Glucagon receptor-Gs complex activated by the small molecule agonist SIM1
4ERS 2.64 Å, A Molecular Basis for Negative Regulation of the Glucagon Receptor
8WG8 2.71 Å, Cryo-EM structures of peptide free and Gs-coupled GCGR
8JIU 2.76 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist SAR425899-bound human GCGR-Gs complex
8YW5 2.84 Å, Cryo-EM structure of the retatrutide-bound human GCGR-Gs complex
8FU6 2.9 Å, GCGR-Gs complex in the presence of RAMP2
8JIT 2.91 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist MEDI0382-bound human GCGR-Gs complex

Browse structure collections

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