5XEZ: Glucagon receptor,Endolysin,Glucagon receptor

Structure of the Full-length glucagon class B G protein-coupled receptor. Determined by X-ray diffraction at 3.0 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Enterobacteria phage T4
Chains: 6
Atoms: 15,068
Mol. weight: 231.98 kDa
Ligands: 97V, NAG
Released: 24 May 2017

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

Secondary structure: helices and β-sheets

5XEZ contains 86 α-helices and 124 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: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	28-48	21
α-helix	51-53	3
β-strand	57-58	2	1
β-strand	61-62	2	2
β-strand	67-68	2	2
β-strand	71-72	2	1
β-strand	75-80	6	3
α-helix	81-82	2
α-helix	88-91	4
β-strand	95-100	6	3
α-helix	101	1
β-strand	106	1	3
α-helix	107	1
β-strand	108	1	4
β-strand	114	1	4
β-strand	117	1	3
β-strand	127-130	4	5
α-helix	132-164	33
α-helix	172-198	27
β-strand	203-206	4	5
β-strand	209-213	5	5
α-helix	218-252	35
α-helix	1003-1010	8
β-strand	1018	1	6
β-strand	1026-1027	2	6
β-strand	1031-1032	2	6
α-helix	1043-1050	8
α-helix	1064-1080	17
α-helix	1085-1090	6
α-helix	1093-1105	13
α-helix	1108-1112	5
α-helix	1115-1122	8
α-helix	1126-1135	10
α-helix	1145-1155	11
α-helix	1159-262	6
α-helix	264-269	6
α-helix	273-289	17
α-helix	309-334	26
α-helix	343-361	19
α-helix	363-367	5
α-helix	378-396	19
α-helix	397-402	6
α-helix	405-414	10

Chain B: 26 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	27-48	22
α-helix	51-53	3
β-strand	57-58	2	7
β-strand	61-62	2	8
β-strand	67-68	2	8
β-strand	71-72	2	7
β-strand	75-80	6	9
α-helix	81-82	2
α-helix	88-91	4
β-strand	95-100	6	9
α-helix	101	1
β-strand	106	1	9
α-helix	107	1
β-strand	108	1	10
β-strand	114	1	10
β-strand	117	1	9
β-strand	127-130	4	11
α-helix	132-163	32
α-helix	172-198	27
β-strand	203-206	4	11
β-strand	209-213	5	11
α-helix	218-254	37
α-helix	1003-1009	7
α-helix	1069-1080	12
α-helix	1085-1090	6
α-helix	1093-1105	13
α-helix	1108-1112	5
α-helix	1115-1122	8
α-helix	1126-1135	10
α-helix	1145-1155	11
α-helix	1159-267	11
α-helix	268-270	3
α-helix	273-289	17
α-helix	309-333	25
α-helix	343-361	19
α-helix	363-366	4
α-helix	378-396	19
α-helix	397-402	6
α-helix	405-414	10

Chain C: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	12
β-strand	225-226	2	13
β-strand	232-239	8	12
α-helix	243-245	3
β-strand	247-253	7	14
β-strand	259-265	7	14
β-strand	272-274	3	14
α-helix	276-278	3
β-strand	279	1	12
β-strand	282-287	6	12
β-strand	292-297	6	12
α-helix	302-304	3
β-strand	306-318	13	14
β-strand	323-332	10	14
β-strand	337-338	2	14
β-strand	339-340	2	13
β-strand	346	1	15
α-helix	347-348	2
β-strand	349-353	5	16
α-helix	357-359	3
β-strand	360-361	2	16
β-strand	364-374	11	16
β-strand	375	1	15
β-strand	380-383	4	17
α-helix	384-386	3
β-strand	388	1	17
β-strand	392-394	3	16
α-helix	395-397	3
β-strand	398-399	2	16
β-strand	405-414	10	16
α-helix	415-417	3
β-strand	418	1	18
β-strand	421	1	18
β-strand	424-429	6	17
α-helix	430-432	3
β-strand	434-439	6	17

Chains D and L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	19-25	7	19
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	85-90	6	20
α-helix	96	1
β-strand	97-98	2	20
β-strand	102-106	5	20
β-strand	111	1	21
α-helix	112-113	2
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153-154	2	23
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-188	6
β-strand	192-197	6	23
β-strand	205-209	5	23

Chain H: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	24
β-strand	225-226	2	25
β-strand	232-239	8	24
α-helix	243-245	3
β-strand	247-253	7	26
β-strand	259-265	7	26
β-strand	272-274	3	26
α-helix	276-278	3
β-strand	282-287	6	24
β-strand	292-297	6	24
α-helix	302-304	3
β-strand	306-318	13	26
β-strand	323-332	10	26
β-strand	337-338	2	26
β-strand	339-340	2	25
α-helix	343-345	3
β-strand	346	1	27
α-helix	347-348	2
β-strand	349-353	5	28
α-helix	357-359	3
β-strand	360-361	2	28
β-strand	364-374	11	28
β-strand	375	1	27
β-strand	380-383	4	29
α-helix	384-386	3
β-strand	388	1	29
β-strand	392-394	3	28
α-helix	395-397	3
β-strand	398-399	2	28
β-strand	405-414	10	28
α-helix	415-417	3
β-strand	418	1	30
β-strand	421	1	30
β-strand	424-429	6	29
α-helix	430-432	3
β-strand	434-439	6	29

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

>5XEZ_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

>5XEZ_2 Antibody, mAb1, heavy chain (chains C, H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVMYYDGSNKDY
VDSVKGRFTISRDNSKNTLYLQMNRLRAEDTAVYYCAREKDHYDILTGYNYYYGLDVWGQ
GTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (D, L), FASTA

>5XEZ_3 Antibody, mAb1, light chain (chains D, L)
DIQMTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLESGVPS
RFSGSGSGTEFTLTISSVQPEDFVTYYCLQHNSNPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

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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