5XF1: Glucagon receptor,Endolysin,Glucagon receptor

Structure of the Full-length glucagon class B G protein-coupled receptor. Determined by X-ray diffraction at 3.19 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 6
Atoms: 15,041
Mol. weight: 232.17 kDa
Ligands: NAG, 97V
Released: 24 May 2017

Explore 5XF1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5XF1 contains 87 α-helices and 129 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: 30 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	28-46	19
α-helix	51-53	3
β-strand	58	1	1
β-strand	61-62	2	2
β-strand	67-68	2	2
β-strand	71	1	1
β-strand	76-80	5	3
α-helix	81-82	2
α-helix	88-91	4
β-strand	95-99	5	3
β-strand	100	1	4
β-strand	106	1	4
α-helix	107	1
β-strand	108	1	5
β-strand	114	1	5
β-strand	117	1	3
β-strand	127-130	4	6
α-helix	132-164	33
α-helix	173-198	26
β-strand	203-206	4	6
β-strand	209-213	5	6
α-helix	218-253	36
α-helix	1003-1010	8
β-strand	1018	1	7
β-strand	1026	1	7
β-strand	1032	1	7
α-helix	1040-1042	3
α-helix	1043-1050	8
α-helix	1064-1079	16
α-helix	1085-1090	6
α-helix	1093-1105	13
α-helix	1108-1111	4
α-helix	1115-1122	8
α-helix	1126-1135	10
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1159-260	4
α-helix	264-271	8
α-helix	273-288	16
α-helix	302	1
α-helix	303-308	6
α-helix	309-333	25
α-helix	343-367	25
α-helix	378-390	13
α-helix	392-397	6
α-helix	398-402	5
α-helix	405-416	12

Chain B: 27 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	27-46	20
α-helix	51-53	3
β-strand	58	1	8
β-strand	61-62	2	9
β-strand	67-68	2	9
β-strand	71	1	8
β-strand	76-80	5	10
α-helix	81-82	2
α-helix	88-91	4
β-strand	95-99	5	10
β-strand	100	1	11
β-strand	106	1	11
α-helix	107	1
β-strand	108	1	12
β-strand	114	1	12
β-strand	117	1	10
β-strand	127-130	4	13
α-helix	132-163	32
α-helix	168-170	3
α-helix	173-198	26
β-strand	203-206	4	13
β-strand	209-213	5	13
α-helix	218-254	37
α-helix	1003-1009	7
α-helix	1067-1079	13
α-helix	1085-1090	6
α-helix	1093-1105	13
α-helix	1108-1111	4
α-helix	1115-1122	8
α-helix	1126-1135	10
α-helix	1137-1141	5
α-helix	1143-1155	13
α-helix	1159-264	8
α-helix	269-288	20
α-helix	303-308	6
α-helix	309-333	25
α-helix	343-367	25
α-helix	377-390	14
α-helix	392-397	6
α-helix	398-402	5
α-helix	405-415	11

Chain C: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	14
β-strand	225-226	2	15
β-strand	228	1	16
β-strand	230	1	16
β-strand	232-239	8	14
β-strand	247-253	7	17
β-strand	259-265	7	17
β-strand	272-274	3	17
α-helix	276-278	3
β-strand	279	1	14
β-strand	282-287	6	14
β-strand	292-297	6	14
α-helix	302-304	3
β-strand	306-318	13	17
β-strand	323-332	10	17
β-strand	336-338	3	17
β-strand	339-340	2	15
α-helix	346-348	3
β-strand	349-353	5	18
β-strand	360-361	2	18
β-strand	364-374	11	18
β-strand	380-383	4	19
α-helix	384-386	3
β-strand	388	1	19
β-strand	392-394	3	18
α-helix	395-397	3
β-strand	398-399	2	18
β-strand	405-414	10	18
β-strand	418	1	20
β-strand	421	1	20
β-strand	424-429	6	19
β-strand	434-439	6	19

Chain D: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	12-13	2	22
α-helix	17-18	2
β-strand	19-25	7	21
β-strand	33-38	6	23
α-helix	43-44	2
β-strand	45-49	5	23
β-strand	53-54	2	23
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	23
α-helix	96	1
β-strand	97-98	2	23
β-strand	102-103	2	23
β-strand	105-106	2	22
β-strand	111	1	24
α-helix	112-113	2
β-strand	114-118	5	25
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	25
β-strand	140	1	24
β-strand	144-150	7	26
β-strand	153-154	2	26
β-strand	159-163	5	25
α-helix	164-167	4
β-strand	173-182	10	25
α-helix	183-188	6
β-strand	191-198	8	26
β-strand	205-210	6	26

Chain H: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	27
β-strand	225-226	2	28
β-strand	228	1	29
β-strand	230	1	29
β-strand	232-239	8	27
β-strand	247-253	7	30
β-strand	259-265	7	30
β-strand	272-274	3	30
α-helix	276-278	3
β-strand	282-287	6	27
β-strand	292-297	6	27
α-helix	302-304	3
β-strand	306-318	13	30
β-strand	323-332	10	30
β-strand	336-338	3	30
β-strand	339-340	2	28
α-helix	346-348	3
β-strand	349-353	5	31
β-strand	360-361	2	31
β-strand	364-374	11	31
β-strand	380	1	32
β-strand	383	1	32
α-helix	384-386	3
β-strand	388	1	32
β-strand	392-394	3	31
α-helix	395-397	3
β-strand	398-399	2	31
β-strand	405-414	10	31
β-strand	418	1	33
β-strand	421	1	33
β-strand	424-429	6	32
β-strand	434-439	6	32

Chain L: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	34
β-strand	12-13	2	35
α-helix	17-18	2
β-strand	19-25	7	34
β-strand	33-38	6	36
α-helix	43-44	2
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	62-67	6	34
β-strand	70-75	6	34
α-helix	80-82	3
β-strand	85-90	6	36
α-helix	96	1
β-strand	97-98	2	36
β-strand	102-103	2	36
β-strand	105-106	2	35
β-strand	111	1	37
α-helix	112-113	2
β-strand	114-118	5	38
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	38
β-strand	140	1	37
β-strand	144-150	7	39
β-strand	153-154	2	39
β-strand	159-163	5	38
α-helix	164-167	4
β-strand	173-182	10	38
α-helix	183-188	6
β-strand	192-198	7	39
β-strand	205-209	5	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glucagon receptor,Endolysin,Glucagon receptor	A, B	protein	574	Homo sapiens, Enterobacteria phage T4	P00720, P47871 (AlphaFold model)
Antibody mAb1 Heavy chain	C, H	protein	231	Homo sapiens
Antibody mAb1 Light chain	D, L	protein	214	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5XF1_1 Glucagon receptor,Endolysin,Glucagon receptor (chains A, B)
GAPQVMDFLFEKWKLYGDQCHHNLSLLPPPTELVCNRTFDKYSCWPDTPANTTANISCPW
YLPWHHKVQHRFVFKRCGPDGQWVRGPRGQPWRDASQCQMDGEEIEVQKEVAKMYSSFQV
MYTVGYSLSLGALLLALAILGGLSKLHCTRNAIHANLFASFVLKASSVLVIDGLLRTRYS
QKIGDDLSVSTWLSDGAVAGCRVAAVFMQYGIVANYCWLLVEGLYLHNLLGLANIFEMLR
IDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFN
QDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDE
AAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYERSFFSLYLGIGWGAPMLFVVPWAVVK
CLFENVQCWTSNDNMGFWWILRFPVFLAILINFFIFVRIVQLLVAKLRARQMHHTDYKFR
LAKSTLTLIPLLGVHEVVFAFVTDEHAQGTLRSAKLFFDLFLSSFQGLLVAVLYCFLNKE
VQSELRRRWHRWRLGKVLWEERNTSNEFLEVLFQ

Sequence of entity 2 (C, H), FASTA

>5XF1_2 Antibody mAb1 Heavy chain (chains C, H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVMYYDGSNKDY
VDSVKGRFTISRDNSKNTLYLQMNRLRAEDTAVYYCAREKDHYDILTGYNYYYGLDVWGQ
GTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (D, L), FASTA

>5XF1_3 Antibody mAb1 Light chain (chains D, L)
DIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLESGVPS
RFSGSGSGTEFTLTISSVQPEDFVTYYCLQHNSNPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
97V	4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl)phenyl]carbamoyl}amino]methyl}-N-(1…	C29 H31 N7 O4 S	2

Primary citation

Structure of the full-length glucagon class B G-protein-coupled receptor. Zhang, H., Qiao, A., Yang, D. et al. Nature (2017) 546:259-264. DOI 10.1038/nature22363 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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