6X1A: Non peptide agonist PF-06882961

Non peptide agonist PF-06882961, bound to Glucagon-Like peptide-1 (GLP-1) Receptor. Determined by electron microscopy at 2.5 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 10,140
Mol. weight: 160.66 kDa
Ligands: UK4
Released: 9 Sept 2020

Explore 6X1A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X1A contains 51 α-helices and 55 β-strands across 5 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: 20 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-37	25
β-strand	40-47	8	1
α-helix	49-51	3
α-helix	53-63	11
α-helix	91-112	22
α-helix	116-119	4
α-helix	127-133	7
α-helix	144-153	10
α-helix	157-166	10
α-helix	175-180	6
α-helix	182-186	5
α-helix	194-199	6
β-strand	207-214	8	1
β-strand	217-224	8	1
α-helix	234-238	5
β-strand	243-248	6	1
α-helix	250-252	3
α-helix	265-277	13
β-strand	286-291	6	1
α-helix	294-302	9
α-helix	308-311	4
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-352	21
β-strand	359-362	4	1
α-helix	371-390	20

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	9-24	16
α-helix	30-33	4
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	91-94	4	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	157-161	5	5
β-strand	166-169	4	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	220-223	4	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	262-264	3	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-307	4	8
β-strand	315-317	3	9
β-strand	320	1	2
β-strand	327-329	3	2
β-strand	330-331	2	9
β-strand	336-339	4	2

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-15	9
α-helix	17-20	4
α-helix	30-33	4
α-helix	45-47	3
α-helix	56-58	3

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-11	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	69-73	5	10
β-strand	78-83	6	10
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-125	4	11

Chain R: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	32-52	21
α-helix	54-56	3
α-helix	61-64	4
β-strand	79-80	2	12
β-strand	83-84	2	13
α-helix	85-86	2
β-strand	99-100	2	13
β-strand	101	1	14
β-strand	103-104	2	12
β-strand	112	1	15
β-strand	119	1	15
α-helix	120	1
β-strand	122	1	14
α-helix	137-166	30
α-helix	175-200	26
α-helix	211-213	3
α-helix	214-222	9
α-helix	224-255	32
α-helix	262-273	12
α-helix	278-290	13
α-helix	298-300	3
α-helix	307-336	30
α-helix	344-360	17
α-helix	364-370	7
α-helix	378-391	14
α-helix	394-399	6
α-helix	400-404	5
α-helix	407-418	12
α-helix	420-422	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	394	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	58	Homo sapiens	P59768 (AlphaFold model)
Nanobody35	N	protein	128	Lama glama
Glucagon-like peptide 1 receptor	R	protein	491	Homo sapiens	P43220 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6X1A_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 2 (B), FASTA

>6X1A_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
QSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>6X1A_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 4 (N), FASTA

>6X1A_4 Nanobody35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS

Sequence of entity 5 (R), FASTA

>6X1A_5 Glucagon-like peptide 1 receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDLEVLFQGPARPQGATVSLWETVQKWREYRRQCQRSLT
EDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWL
QKDNSSLPWRDLSECEESKRGERSSPEEQLLFLYIIYTVGYALSFSALVIASAILLGFRH
LHCTRNYIHLNLFASFILRALSVFIKDAALKWMYSTAAQQHQWDGLLSYQDSLSCRLVFL
LMQYCVAANYYWLLVEGVYLYTLLAFSVFSEQWIFRLYVSIGWGVPLLFVVPWGIVKYLY
EDEGCWTRNSNMNYWLIIRLPILFAIGVNFLIFVRVICIVVSKLKANLMCKTDIKCRLAK
STLTLIPLLGTHEVIFAFVMDEHARGTLRFIKLFTELSFTSFQGLMVAILYCFVNNEVQL
EFRKSWERWRLEHLHIQRDSSMKPLKCPTSSLSSGATAGSSMYTATCQASCSPAGLEVLF
QGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
UK4	2-[(4-{6-[(4-cyano-2-fluorophenyl)methoxy]pyridin-2-yl}piperidin-1-yl)methyl]-1…	C31 H30 F N5 O4	1

Primary citation

Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists. Zhang, X., Belousoff, M.J., Zhao, P. et al. Mol Cell (2020) 80:485. DOI 10.1016/j.molcel.2020.09.020 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
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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