8YKT: Fab and SEB complex

Fab and SEB complex. Determined by X-ray diffraction at 2.04 Å resolution. Released 12 Mar 2025.

Method: X-ray diffraction
Resolution: 2.04 Å
Organisms: Staphylococcus aureus, Homo sapiens
Chains: 3
Atoms: 5,578
Mol. weight: 76.03 kDa
Released: 12 Mar 2025

Explore 8YKT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YKT contains 24 α-helices and 67 β-strands across 3 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: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	13-14	2
α-helix	15-17	3
β-strand	18	1	1
α-helix	23-26	4
α-helix	27-29	3
β-strand	34-39	6	2
β-strand	43	1	3
β-strand	49-52	4	3
β-strand	64-68	5	3
α-helix	72-78	7
β-strand	83-87	5	2
β-strand	90	1	3
β-strand	112-116	5	3
β-strand	119-121	3	2
β-strand	126-139	14	4
β-strand	142-153	12	4
β-strand	155-157	3	5
α-helix	158-173	16
β-strand	183-191	9	4
β-strand	196-200	5	4
α-helix	203-204	2
β-strand	206	1	1
α-helix	211-215	5
α-helix	216-218	3
β-strand	223-225	3	5
β-strand	230-237	8	4

Chain H: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
β-strand	12-13	2	7
β-strand	19-26	8	6
α-helix	30-32	3
β-strand	35-40	6	8
β-strand	46-52	7	8
β-strand	59-61	3	8
β-strand	69-74	6	6
β-strand	79-84	6	6
α-helix	89-91	3
β-strand	93-99	7	8
β-strand	105-106	2	4
β-strand	113-114	2	8
β-strand	119-121	3	8
β-strand	122-123	2	7
β-strand	129	1	9
α-helix	130-131	2
β-strand	132-136	5	10
α-helix	137-139	3
β-strand	147-157	11	10
β-strand	158	1	9
β-strand	163-166	4	11
α-helix	167-169	3
β-strand	171	1	11
β-strand	175-177	3	10
α-helix	178-180	3
β-strand	181-182	2	10
β-strand	188-197	10	10
α-helix	198-200	3
β-strand	206-212	7	11
α-helix	213-215	3
β-strand	217-223	7	11

Chain L: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	12
β-strand	6	1	13
β-strand	10-13	4	14
β-strand	19-24	6	13
β-strand	33	1	4
β-strand	36-40	5	14
β-strand	47-50	4	14
β-strand	51	1	15
β-strand	55	1	15
β-strand	64-69	6	13
β-strand	72-77	6	13
α-helix	82-84	3
β-strand	86-94	9	14
β-strand	99-102	4	14
β-strand	103	1	12
β-strand	106-110	5	14
β-strand	116	1	16
α-helix	117-118	2
β-strand	119-123	5	17
α-helix	124-126	3
α-helix	127-131	5
β-strand	135-144	10	17
β-strand	145	1	16
β-strand	150-155	6	18
β-strand	158-160	3	18
β-strand	164-166	3	17
α-helix	167-169	3
β-strand	170-171	2	17
β-strand	177-185	9	17
α-helix	187-192	6
β-strand	196-202	7	18
β-strand	205-211	7	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enterotoxin type B	A	protein	239	Staphylococcus aureus	P01552 (AlphaFold model)
Fab Heavy chain	H	protein	232	Homo sapiens
Fab Light chain	L	protein	217	Homo sapiens

Sequence of entity 1 (A), FASTA

>8YKT_1 Enterotoxin type B (chains A)
ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFRYFDLIYSIKDTKLGN
YDNVRVEFKNKDLADKYKDKYVDVFGANAYYQCAFSKKTNDINSHQTDKRKTCMYGGVTE
HNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNS
PYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

Sequence of entity 2 (H), FASTA

>8YKT_2 Fab Heavy chain (chains H)
DEVQLVESGGGVVQPGKSLRLSCAASGFTFSNYGMHWVRQAPGKGLEWVAVISYDGSDKF
YADSVKGRFTVSRDTSKNTLFLQMNSLIPEDTAVYYCAKDPYPSQRAPWNWVDPRGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>8YKT_3 Fab Light chain (chains L)
DQSVLTQPPSVSAAPGQKVTISCSGNSSNIGQNHVSWYQQVPGKAPKVLIYDTKERPSGI
PDRFSGSRSGTSVTLGITGLQTGDEADYYCGTWDSRLSAVVFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Structure of Staphylococcal Enterotoxin B mutant in complex with a neutralization antibody Fab fragment. Fan, H.Y., Zeng, H. To be published.

Other PDB entries of the same protein (UniProt P01552 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SEB 1.48 Å, Staphylococcal enterotoxin B
8YBO 1.59 Å, Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB)
4RGO 1.8 Å, Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8
1SE4 1.9 Å, Staphylococcal enterotoxin B complexed with lactose
3GP7 1.9 Å, Staphylococcal Enterotoxin B mutant N23YK97SK98S
1D5M 2.0 Å, X-ray crystal structure of HLA-DR4 complexed with peptide and seb
1D5Z 2.0 Å, X-ray crystal structure of HLA-DR4 complexed with peptidomimetic and seb
1GOZ 2.0 Å, Structural basis for the altered T-cell receptor binding specificty in a superantigenic…
8YBM 2.04 Å, Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB)
8YBP 2.08 Å, Crystal structure of nanobody SEB-Nb20 bound to staphylococcal enterotoxin B (SEB)
8YBN 2.18 Å, Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)
1SE3 2.3 Å, Staphylococcal enterotoxin B complexed with GM3 trisaccharide

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