8YX1: CD40

CD40 in complex with Bleselumab Fab. Determined by X-ray diffraction at 2.7 Å resolution. Released 8 May 2024.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,837
Mol. weight: 134.94 kDa
Released: 8 May 2024

Explore 8YX1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YX1 contains 51 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: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	1-5	5	21
β-strand	9-10	2	22
α-helix	14-15	2
β-strand	16-23	8	21
β-strand	33-39	7	23
β-strand	46-52	7	23
β-strand	57-59	3	23
α-helix	64-66	3
β-strand	67-72	6	21
α-helix	73-75	3
β-strand	77-82	6	21
α-helix	87-89	3
β-strand	91-101	11	23
β-strand	104-109	6	23
β-strand	113-115	3	23
β-strand	116-117	2	22
α-helix	121-122	2
β-strand	123	1	24
α-helix	124-125	2
β-strand	126-130	5	25
β-strand	141-151	11	25
β-strand	152	1	24
β-strand	156-160	5	26
α-helix	161-163	3
β-strand	169-171	3	25
α-helix	172-174	3
β-strand	175-176	2	25
β-strand	182-191	10	25
α-helix	192-194	3
β-strand	201-206	6	26
β-strand	211-216	6	26

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	27
β-strand	10-14	5	28
β-strand	19-25	7	27
β-strand	33-38	6	28
β-strand	45-49	5	28
β-strand	53-54	2	28
α-helix	55	1
β-strand	62-67	6	27
β-strand	70-75	6	27
α-helix	80-82	3
β-strand	84-90	7	28
β-strand	96-97	2	28
β-strand	101-106	6	28
β-strand	110	1	29
α-helix	111-112	2
β-strand	113-117	5	30
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	30
β-strand	139	1	29
β-strand	144-149	6	31
β-strand	152-153	2	31
β-strand	158-162	5	30
α-helix	163-166	4
β-strand	172-181	10	30
α-helix	182-187	6
β-strand	191-196	6	31
β-strand	204-208	5	31

Chain C: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	32
β-strand	16-19	4	32
α-helix	20	1
β-strand	21	1	33
α-helix	22	1
β-strand	25-29	5	34
β-strand	38-41	4	34
β-strand	46-47	2	35
β-strand	52	1	33
α-helix	57	1
β-strand	58-59	2	35
α-helix	60-62	3
α-helix	65-67	3
β-strand	69-73	5	36
β-strand	76	1	37
β-strand	79	1	37
β-strand	82-85	4	36
α-helix	86	1
β-strand	89-91	3	38
β-strand	99-101	3	38
α-helix	102-103	2
β-strand	105	1	39
β-strand	109-113	5	40
α-helix	120-121	2
β-strand	122-125	4	40
β-strand	130-131	2	41
β-strand	136	1	39
α-helix	139-141	3
β-strand	142-143	2	41
α-helix	144-145	2

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	1-5	5	1
β-strand	9-10	2	2
α-helix	15	1
β-strand	16-23	8	1
β-strand	33-39	7	3
β-strand	46-52	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	87-89	3
β-strand	91-101	11	3
β-strand	104-109	6	3
β-strand	113-115	3	3
β-strand	116-117	2	2
α-helix	121-122	2
β-strand	123	1	4
α-helix	124-125	2
β-strand	126-130	5	5
β-strand	141-151	11	5
β-strand	152	1	4
β-strand	157-160	4	6
α-helix	161-163	3
β-strand	169-171	3	5
α-helix	172-174	3
β-strand	175-176	2	5
β-strand	182-191	10	5
α-helix	192-194	3
β-strand	200-206	7	6
α-helix	207-209	3
β-strand	211-217	7	6

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
β-strand	96-97	2	8
β-strand	101-106	6	8
β-strand	110	1	9
α-helix	111-112	2
β-strand	113-117	5	10
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	10
β-strand	139	1	9
β-strand	144-149	6	11
β-strand	152-153	2	11
α-helix	154	1
β-strand	158-162	5	10
β-strand	172-181	10	10
α-helix	182-186	5
β-strand	190-196	7	11
β-strand	204-209	6	11

Chain R: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	12
β-strand	16-19	4	12
α-helix	20	1
β-strand	21	1	13
α-helix	22	1
β-strand	25-29	5	14
β-strand	38-41	4	14
β-strand	46-47	2	15
β-strand	52	1	13
α-helix	57	1
β-strand	58-59	2	15
α-helix	60-62	3
α-helix	65-67	3
β-strand	69-73	5	16
β-strand	82-85	4	16
α-helix	86	1
β-strand	89-91	3	17
β-strand	99-101	3	17
α-helix	102-103	2
β-strand	105	1	18
β-strand	109-113	5	19
α-helix	120-121	2
β-strand	122-125	4	19
β-strand	130-131	2	20
β-strand	136	1	18
β-strand	142-143	2	20
α-helix	144-146	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bleselumab, heavy chain	A, H	protein	229	Homo sapiens
Bleselumab, light chain	B, L	protein	213	Homo sapiens
Tumor necrosis factor receptor superfamily member 5	C, R	protein	179	Homo sapiens	P25942 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8YX1_1 Bleselumab, heavy chain (chains A, H)
LQLQESGPGLLKPSETLSLTCTVSGGSISSPGYYGGWIRQPPGKGLEWIGSIYKSGSTYH
NPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCTRPVVRYFGWFDPWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Sequence of entity 2 (B, L), FASTA

>8YX1_2 Bleselumab, light chain (chains B, L)
AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASNLESGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQFNSYPTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, R), FASTA

>8YX1_3 Tumor necrosis factor receptor superfamily member 5 (chains C, R)
EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQH
KYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSD
TICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDRLRHHHHHH

Primary citation

Crystal structures of human CD40 in complex with monoclonal antibodies dacetuzumab and bleselumab. Asano, R., Nakakido, M., Perez, J.F. et al. Biochem Biophys Res Commun (2024) 714:149969-149969. DOI 10.1016/j.bbrc.2024.149969 · PubMed

Other PDB entries of the same protein (UniProt P25942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LB6 1.8 Å, TRAF6-CD40 Complex
1D00 2.0 Å, Structure of tnf receptor associated factor 2 in complex with a 5-residue CD40 peptide
7P3I 2.29 Å, Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein
1CZZ 2.7 Å, Structure of tnf receptor associated factor 2 in complex with a 17-residue CD40 peptide
5DMJ 2.79 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB
8YX9 2.8 Å, CD40 in complex with Dacetuzumab Fab
6PE8 2.84 Å, Crystal structure of CD40/ABBV-323 FAB complex
6FAX 2.99 Å, Complex of Human CD40 Ectodomain with Lob 7.4 Fab
6PE9 3.13 Å, Crystal Structure of CD40 complexed to FAB516
5IHL 3.3 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 dab
1FLL 3.5 Å, Molecular basis for CD40 signaling mediated by TRAF3
3QD6 3.5 Å, Crystal structure of the CD40 and CD154 (CD40L) complex

Browse structure collections

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