5HYS: IgE

Structure of IgE complexed with omalizumab. Determined by X-ray diffraction at 2.5 Å resolution. Released 1 Jun 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 12
Atoms: 20,626
Mol. weight: 301.11 kDa
Released: 1 Jun 2016

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

Secondary structure: helices and β-sheets

5HYS contains 108 α-helices and 256 β-strands across 12 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
β-strand	34-40	7	12
β-strand	46-53	8	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-102	11	12
β-strand	105-111	7	12
β-strand	115-119	5	12
β-strand	125	1	13
α-helix	126-127	2
β-strand	128-132	5	14
α-helix	133-135	3
β-strand	143-153	11	14
β-strand	154	1	13
β-strand	159-162	4	15
α-helix	163-165	3
β-strand	167	1	15
β-strand	171-173	3	14
α-helix	174-176	3
β-strand	177-178	2	14
β-strand	184-193	10	14
α-helix	196-199	4
β-strand	203-208	6	15
α-helix	209-211	3
β-strand	213-218	6	15

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	2
β-strand	19-25	7	16
β-strand	30-31	2	17
β-strand	34-35	2	17
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
α-helix	59	1
β-strand	66-71	6	16
β-strand	74-79	6	16
α-helix	84-86	3
β-strand	88-94	7	2
α-helix	100	1
β-strand	101-102	2	2
β-strand	106-111	6	2
β-strand	115	1	18
α-helix	116-117	2
β-strand	118-122	5	19
α-helix	123-125	3
α-helix	128-130	3
β-strand	133-143	11	19
β-strand	144	1	18
β-strand	149-154	6	20
β-strand	157-158	2	20
β-strand	163-167	5	19
α-helix	168-171	4
β-strand	177-186	10	19
α-helix	187-192	6
β-strand	195-201	7	20
β-strand	209-214	6	20

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	10-12	3	22
β-strand	18-25	8	21
β-strand	34-40	7	22
β-strand	46-53	8	22
β-strand	58-60	3	22
β-strand	68-73	6	21
α-helix	74-76	3
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-102	11	22
β-strand	105-111	7	22
β-strand	115-119	5	22
β-strand	125	1	23
α-helix	126-127	2
β-strand	128-132	5	24
β-strand	139-140	2	24
β-strand	143-153	11	24
β-strand	154	1	23
β-strand	159-162	4	25
α-helix	163-165	3
β-strand	167	1	25
β-strand	171-173	3	24
α-helix	174-176	3
β-strand	177-178	2	24
β-strand	184-193	10	24
α-helix	196-199	4
β-strand	202-208	7	25
α-helix	209-211	3
β-strand	213-219	7	25

Chain D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-14	5	22
β-strand	19-25	7	26
β-strand	30-31	2	27
β-strand	34-35	2	27
β-strand	37-42	6	22
β-strand	49-53	5	22
β-strand	57-58	2	22
α-helix	59	1
β-strand	66-71	6	26
β-strand	74-79	6	26
α-helix	84-86	3
β-strand	88-94	7	22
α-helix	100	1
β-strand	101-102	2	22
β-strand	106-111	6	22
β-strand	115	1	28
α-helix	116-117	2
β-strand	118-122	5	29
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	29
β-strand	144	1	28
β-strand	148-154	7	30
β-strand	157-158	2	30
β-strand	163-167	5	29
α-helix	168-171	4
β-strand	177-186	10	29
α-helix	187-192	6
β-strand	195-202	8	30
β-strand	209-214	6	30

Chain E: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	10-12	3	22
β-strand	18-25	8	31
β-strand	34-40	7	22
β-strand	46-53	8	22
β-strand	58-60	3	22
β-strand	68-73	6	31
α-helix	74-76	3
β-strand	78-83	6	31
α-helix	88-90	3
β-strand	92-102	11	22
β-strand	105-111	7	22
β-strand	115-119	5	22
β-strand	125	1	32
α-helix	126-127	2
β-strand	128-132	5	33
β-strand	143-153	11	33
β-strand	154	1	32
β-strand	159-162	4	34
β-strand	167	1	34
β-strand	171-173	3	33
α-helix	174-176	3
β-strand	177-178	2	33
β-strand	184-193	10	33
α-helix	196-199	4
β-strand	203-208	6	34
α-helix	209-211	3
β-strand	213-218	6	34

Chain F: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-14	5	22
β-strand	19-25	7	35
β-strand	30-31	2	36
β-strand	34-35	2	36
β-strand	37-42	6	22
β-strand	49-53	5	22
β-strand	57-58	2	22
α-helix	59	1
β-strand	66-71	6	35
β-strand	74-79	6	35
α-helix	84-86	3
β-strand	88-94	7	22
α-helix	100	1
β-strand	101-102	2	22
β-strand	106-111	6	22
β-strand	115	1	37
α-helix	116-117	2
β-strand	118-122	5	38
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	38
β-strand	144	1	37
β-strand	149-154	6	39
β-strand	157-158	2	39
β-strand	163-167	5	38
α-helix	168-171	4
β-strand	177-186	10	38
α-helix	187-192	6
β-strand	195-201	7	39
β-strand	209-214	6	39

Chain G: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	337-340	4	40
α-helix	341-344	4
α-helix	345-349	5
β-strand	355-363	9	40
α-helix	368-370	3
β-strand	371-376	6	41
α-helix	380-383	4
β-strand	386-391	6	40
β-strand	397-404	8	40
α-helix	407-412	6
β-strand	415-421	7	41
β-strand	429-434	6	41
β-strand	441	1	42
α-helix	442-443	2
β-strand	444-449	6	43
α-helix	450-452	3
β-strand	459-469	11	43
β-strand	470	1	42
β-strand	475-480	6	44
β-strand	483-484	2	44
α-helix	485-486	2
α-helix	487-489	3
β-strand	490-492	3	43
α-helix	493-495	3
β-strand	496-497	2	43
β-strand	503-512	10	43
α-helix	513-518	6
β-strand	522-527	6	44
β-strand	536-541	6	44

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-40	7	2
β-strand	46-53	8	2
β-strand	58-60	3	2
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-102	11	2
β-strand	105-111	7	2
β-strand	115-119	5	2
α-helix	123-124	2
β-strand	125	1	3
α-helix	126-127	2
β-strand	128-132	5	4
α-helix	136-138	3
β-strand	139-140	2	4
β-strand	143-153	11	4
β-strand	154	1	3
β-strand	159-162	4	5
α-helix	163-165	3
β-strand	167	1	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-178	2	4
β-strand	184-193	10	4
α-helix	196-199	4
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epididymis luminal protein 214	A, C, E, H	protein	222	Homo sapiens
Uncharacterized protein	B, D, F, L	protein	218	Homo sapiens
Ig epsilon chain C region	G, I, J, K	protein	230	Homo sapiens	P01854 (AlphaFold model)

Sequence of entity 1 (A, C, E, H), FASTA

>5HYS_1 Epididymis luminal protein 214 (chains A, C, E, H)
EVQLVESGGGLVQPGGSLRLSCAVSGYSITSGYSWNWIRQAPGKGLEWVASITYDGSTNY
NPSVKGRITISRDDSKNTFYLQMNSLRAEDTAVYYCARGSHYFGHWHFAVWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 2 (B, D, F, L), FASTA

>5HYS_2 Uncharacterized protein (chains B, D, F, L)
DIQLTQSPSSLSASVGDRVTITCRASQSVDYDGDSYMNWYQQKPGKAPKLLIYAASYLES
GVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSHEDPYTFGQGTKVEIKRTVAAPSVF
IFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS
STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (G, I, J, K), FASTA

>5HYS_3 Ig epsilon chain C region (chains G, I, J, K)
ADPAADSNPRCVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNH
STRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPE
VYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFF
VFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPGKAADDDDK

Primary citation

Structural basis of omalizumab therapy and omalizumab-mediated IgE exchange. Pennington, L.F., Tarchevskaya, S., Brigger, D. et al. Nat Commun (2016) 7:11610-11610. DOI 10.1038/ncomms11610 · PubMed

Other PDB entries of the same protein (UniProt P01854 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MOL 1.75 Å, Human IgE-Fc crystal structure
2WQR 1.9 Å, The high resolution crystal structure of IgE Fc
5MOK 2.0 Å, Crystal structure of human IgE-Fc epsilon 3-4
5MOI 2.2 Å, Crystal structure of human IgE-Fc epsilon 3-4
3H9Y 2.23 Å, Crystal structure of the IgE-Fc3-4 domains
5MOJ 2.26 Å, Crystal structure of IgE-Fc epsilon 3-4
1FP5 2.3 Å, Crystal structure analysis of the human IgE-fc CEPSILON3-CEPSILON4 fragment.
30AF 2.4 Å, Complex between IgE-Fc and anti-IgE Fab aeFab98
3H9Z 2.45 Å, Crystal structure of the IgE-Fc3-4 domains
1O0V 2.6 Å, The crystal structure of IgE Fc reveals an asymmetrically bent conformation
5LGJ 2.6 Å, The crystal structure of IgE fc mutant - P333C
4GT7 2.61 Å, An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor…

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