5TUD: PDB entry 5TUD

Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody. Determined by X-ray diffraction at 3.0 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Escherichia coli, Mus musculus
Chains: 6
Atoms: 12,395
Mol. weight: 201.43 kDa
Ligands: ERM
Released: 26 Jul 2017

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

Secondary structure: helices and β-sheets

5TUD contains 58 α-helices and 99 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: 17 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	57-81	25
α-helix	88-102	15
α-helix	103-107	5
α-helix	108-116	9
α-helix	127-158	32
α-helix	168-187	20
α-helix	189-192	4
β-strand	195-197	3	1
α-helix	202-204	3
α-helix	215-222	8
α-helix	223-227	5
α-helix	228-1016	37
α-helix	1023-1040	18
α-helix	1059-1080	22
α-helix	1084-336	46
α-helix	338-349	12
α-helix	355-379	25
α-helix	385-395	11

Chain B: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	2
β-strand	10-13	4	3
β-strand	20-25	6	2
β-strand	33-37	5	3
β-strand	44-48	5	3
β-strand	52-53	2	3
β-strand	61-65	5	2
β-strand	69-74	6	2
α-helix	79-81	3
β-strand	84-88	5	3
α-helix	95	1
β-strand	96	1	4
β-strand	97	1	3
β-strand	98	1	2
β-strand	102-105	4	3
β-strand	110	1	5
β-strand	113-117	5	6
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	6
β-strand	139	1	5
β-strand	144-149	6	7
β-strand	153	1	7
β-strand	158-162	5	6
α-helix	163-166	4
β-strand	172-181	10	6
α-helix	182-185	4
β-strand	190-196	7	7
β-strand	204-205	2	7
β-strand	208-209	2	7

Chain C: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	9
β-strand	18-25	8	8
β-strand	34-40	7	4
β-strand	44-51	8	4
β-strand	58-60	3	4
β-strand	68-73	6	8
β-strand	78-83	6	8
β-strand	93-98	6	4
β-strand	102-104	3	1
β-strand	109-111	3	1
β-strand	116-117	2	4
α-helix	118-120	3
β-strand	121-122	2	4
β-strand	123-125	3	9
α-helix	129-130	2
β-strand	134-138	5	10
β-strand	150-157	8	10
β-strand	159	1	11
β-strand	164-168	5	12
β-strand	173	1	12
β-strand	177-179	3	10
α-helix	180-182	3
β-strand	183-184	2	11
β-strand	190-191	2	11
β-strand	193-198	6	10
α-helix	202-205	4
β-strand	209-214	6	12
β-strand	219-224	6	12
α-helix	227-230	4

Chain D: 18 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	56-81	26
α-helix	83-85	3
α-helix	88-102	15
α-helix	103-107	5
α-helix	108-116	9
α-helix	127-158	32
α-helix	168-187	20
α-helix	189-192	4
β-strand	195-197	3	13
α-helix	202-204	3
α-helix	215-222	8
α-helix	223-227	5
α-helix	228-1017	38
α-helix	1023-1043	21
α-helix	1060-1080	21
α-helix	1084-336	46
α-helix	338-349	12
α-helix	355-379	25
α-helix	385-395	11

Chain E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-13	4	15
β-strand	19-25	7	14
β-strand	33-37	5	15
β-strand	44-49	6	15
β-strand	52-53	2	15
β-strand	61-65	5	14
β-strand	69-74	6	14
α-helix	79-81	3
β-strand	84-89	6	15
α-helix	95	1
β-strand	96-97	2	15
β-strand	98	1	14
β-strand	101-105	5	15
β-strand	110	1	16
β-strand	113-117	5	17
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	17
β-strand	139	1	16
β-strand	144-149	6	18
β-strand	152-153	2	18
α-helix	154	1
β-strand	158-162	5	17
α-helix	163-166	4
β-strand	172-181	10	17
α-helix	182-185	4
β-strand	190-196	7	18
β-strand	204-209	6	18

Chain F: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
α-helix	7-9	3
β-strand	10-12	3	20
β-strand	18-20	3	19
β-strand	22-25	4	19
β-strand	34-40	7	21
β-strand	44-51	8	21
β-strand	58-60	3	21
β-strand	68-73	6	19
β-strand	78-83	6	19
β-strand	93-98	6	21
β-strand	102-104	3	13
β-strand	109-111	3	13
β-strand	116-117	2	21
α-helix	118-120	3
β-strand	121-122	2	21
β-strand	123-125	3	20
α-helix	129-130	2
β-strand	131	1	22
β-strand	134-137	4	23
α-helix	142-144	3
β-strand	149-157	9	23
β-strand	159	1	23
β-strand	160	1	22
β-strand	164-168	5	24
β-strand	173	1	24
β-strand	177-184	8	23
β-strand	190-199	10	23
α-helix	202-205	4
β-strand	209-214	6	24
β-strand	219-224	6	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera	A, D	protein	457	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), P41595 (AlphaFold model)
Anti-5-HT2B Fab light chain	B, E	protein	213	Mus musculus
Anti-5-HT2B Fab heavy chain	C, F	protein	236	Mus musculus

Sequence of entity 1 (A, D), FASTA

>5TUD_1 5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera (chains A, D)
MKTIIALSYIFCLVFADYKDDDDGAPTESIPEEMKQIVEEQGNKLHWAALLILMVIIPTI
GGNTLVILAVSLEKKLQYATNYFLMSLAVADLLVGLFVMPIALLTIMFEAMWPLPLVLCP
AWLFLDVLFSTASIWHLCAISVDRYIAIKKPIQANQYNSRATAFIKITVVWLISIGIAIP
VPIKGIETDVDNPNNITCVLTKERFGDFMLFGSLAAFFTPLAIMIVTYFLTIHALQKKAA
DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDF
RHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLQTISNEQRASKVLGI
VFFLFLLMWCPFFITNITLVLCDSCNQTTLQMLLEIFVWIGYVSSGVNPLVYTLFNKTFR
DAFGRYITCNYRATKSVGRPLEVLFQGPHHHHHHHHH

Sequence of entity 2 (B, E), FASTA

>5TUD_2 Anti-5-HT2B Fab light chain (chains B, E)
DIVLIQSPAIMSASPGEKVTITCSASSSVSYMHWFQQKPGTSPKLWIYSTSNLASGVPAR
FSGSGSGTSYSLTISRMEAEDAATYYCQQRSSYPLTFGAGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSLPVTKSFNRGEC

Sequence of entity 3 (C, F), FASTA

>5TUD_3 Anti-5-HT2B Fab heavy chain (chains C, F)
EVQLQQSGPELVKPGASVKLSCKASGYTFTSSWMHWVKQRPGQGLEWIGNIYPSNGGTNY
NERFKSKATLTVDRSSNTAYMQLSSLTSEDSAVYFCARFGSFITTILTTYYNPVDYWGQG
TTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ERM	Ergotamine	C33 H35 N5 O5	2

Primary citation

Structural insights into the extracellular recognition of the human serotonin 2B receptor by an antibody. Ishchenko, A., Wacker, D., Kapoor, M. et al. Proc Natl Acad Sci U S A (2017) 114:8223-8228. DOI 10.1073/pnas.1700891114 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

Browse structure collections

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