8YX9: CD40

CD40 in complex with Dacetuzumab Fab. Determined by X-ray diffraction at 2.8 Å resolution. Released 8 May 2024.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 12
Atoms: 16,889
Mol. weight: 272.25 kDa
Released: 8 May 2024

Explore 8YX9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YX9 contains 104 α-helices and 241 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: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	48
β-strand	36-39	4	48
α-helix	40	1
β-strand	41	1	49
α-helix	42	1
β-strand	45-49	5	50
β-strand	58-61	4	50
β-strand	66-67	2	51
β-strand	72	1	49
α-helix	77	1
β-strand	78-79	2	51
α-helix	80-82	3
α-helix	85-87	3
β-strand	89-93	5	52
α-helix	100-101	2
β-strand	102-105	4	52
β-strand	109-111	3	53
β-strand	119-121	3	53
α-helix	122-124	3
β-strand	125	1	54
β-strand	129-133	5	55
β-strand	142-145	4	55
β-strand	150-151	2	56
β-strand	156	1	54
α-helix	161	1
β-strand	162-163	2	56
α-helix	164-166	3

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	58-60	3	15
α-helix	62-64	3
β-strand	68-73	6	14
α-helix	74-76	3
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-98	7	15
β-strand	108-112	5	15
β-strand	118	1	16
α-helix	119-120	2
β-strand	121-125	5	17
α-helix	126-128	3
β-strand	136-146	11	17
β-strand	147	1	16
β-strand	152-155	4	18
α-helix	156-158	3
β-strand	160	1	18
β-strand	164-166	3	17
α-helix	167-169	3
β-strand	171	1	17
β-strand	177-186	10	17
β-strand	195-201	7	18
α-helix	202-204	3
β-strand	206-212	7	18

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	19
β-strand	10-14	5	20
β-strand	19-25	7	19
β-strand	30	1	21
β-strand	36	1	21
β-strand	38-43	6	20
α-helix	48-49	2
β-strand	50-54	5	20
β-strand	58-59	2	20
β-strand	67-72	6	19
β-strand	75-80	6	19
α-helix	85-87	3
β-strand	89-95	7	20
α-helix	101	1
β-strand	102-103	2	20
β-strand	107-112	6	20
β-strand	116	1	22
α-helix	117-118	2
β-strand	119-123	5	23
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	23
β-strand	145	1	22
β-strand	150-155	6	24
β-strand	158-159	2	24
β-strand	164-168	5	23
α-helix	169-172	4
β-strand	178-187	10	23
α-helix	188-193	6
β-strand	196-202	7	24
β-strand	210-215	6	24

Chain D: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	57
β-strand	37-39	3	57
α-helix	40	1
β-strand	41	1	58
α-helix	42	1
β-strand	45-49	5	59
α-helix	56-57	2
β-strand	58-61	4	59
β-strand	66-67	2	60
β-strand	72	1	58
α-helix	77	1
β-strand	78-79	2	60
α-helix	80-81	2
α-helix	85-87	3
β-strand	89-93	5	61
β-strand	102-105	4	61
α-helix	106	1
β-strand	109-111	3	62
β-strand	119-121	3	62
α-helix	122-124	3
β-strand	133	1	63
β-strand	142	1	63

Chain E: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	10-12	3	26
β-strand	18-25	8	25
α-helix	29-31	3
β-strand	34-39	6	26
β-strand	45-52	8	26
β-strand	57-60	4	26
α-helix	62-64	3
β-strand	68-73	6	25
α-helix	74-76	3
β-strand	78-83	6	25
α-helix	88-90	3
β-strand	92-98	7	26
β-strand	108-112	5	26
β-strand	118	1	27
α-helix	119-120	2
β-strand	121-125	5	28
β-strand	136-146	11	28
β-strand	147	1	27
β-strand	152-155	4	29
α-helix	156-158	3
β-strand	165-166	2	28
α-helix	167-169	3
β-strand	170-171	2	28
β-strand	177-186	10	28
α-helix	187-189	3
β-strand	190	1	30
β-strand	193	1	30
β-strand	196-201	6	29
α-helix	202-204	3
β-strand	206-211	6	29

Chain F: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	31
β-strand	10-14	5	20
β-strand	19-25	7	31
β-strand	30	1	32
β-strand	36	1	32
β-strand	38-43	6	20
α-helix	48-49	2
β-strand	50-54	5	20
β-strand	58-59	2	20
β-strand	67-72	6	31
β-strand	75-80	6	31
α-helix	85-87	3
β-strand	89-95	7	20
α-helix	101	1
β-strand	102-103	2	20
β-strand	107-112	6	20
β-strand	116	1	33
α-helix	117-118	2
β-strand	119-123	5	34
α-helix	124-126	3
α-helix	129-132	4
β-strand	134-144	11	34
β-strand	145	1	33
β-strand	150-155	6	35
β-strand	158-159	2	35
α-helix	160	1
β-strand	164-168	5	34
α-helix	169-172	4
β-strand	178-187	10	34
α-helix	188-193	6
β-strand	196-202	7	35
β-strand	210-215	6	35

Chain G: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	18-24	7	36
α-helix	29-31	3
β-strand	34-39	6	37
β-strand	46-52	7	37
β-strand	57-60	4	37
α-helix	62-64	3
β-strand	68-73	6	36
α-helix	74-76	3
β-strand	78-83	6	36
α-helix	88-90	3
β-strand	92-98	7	37
β-strand	108-110	3	37
β-strand	118	1	38
β-strand	121-125	5	39
α-helix	126-128	3
β-strand	136-146	11	39
β-strand	147	1	38
β-strand	152-155	4	40
α-helix	156-158	3
β-strand	160	1	40
β-strand	164-166	3	39
α-helix	167-169	3
β-strand	171	1	39
β-strand	177-186	10	39
α-helix	187-189	3
β-strand	190	1	41
β-strand	193	1	41
β-strand	195-200	6	40
α-helix	202-204	3
β-strand	208-212	5	40

Chain H: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	108-110	3	3
β-strand	111-112	2	2
β-strand	118	1	4
α-helix	119-120	2
β-strand	121-125	5	5
α-helix	126-128	3
β-strand	136-146	11	5
β-strand	147	1	4
β-strand	152-155	4	6
α-helix	156-158	3
β-strand	160	1	6
β-strand	164-166	3	5
α-helix	167-169	3
β-strand	171	1	5
β-strand	177-186	10	5
α-helix	187-189	3
β-strand	190	1	7
β-strand	193	1	7
β-strand	195-201	7	6
β-strand	206-212	7	6

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
Dacetuzumab, Heavy chain	B, E, G, H	protein	223	Homo sapiens
Dacetuzumab, light chain	C, F, I, L	protein	219	Homo sapiens
Tumor necrosis factor receptor superfamily member 5	A, D, J, K	protein	179	Homo sapiens	P25942 (AlphaFold model)

Sequence of entity 1 (B, E, G, H), FASTA

>8YX9_1 Dacetuzumab, Heavy chain (chains B, E, G, H)
EVQLVESGGGLVQPGGSLRLSCAASGYSFTGYYIHWVRQAPGKGLEWVARVIPNAGGTSY
NQKFKGRFTLSVDNSKNTAYLQMNSLRAEDTAVYYCAREGIYWWGQGTLVTVSSASTKGP
SVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS
SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Sequence of entity 2 (C, F, I, L), FASTA

>8YX9_2 Dacetuzumab, light chain (chains C, F, I, L)
DIQMTQSPSSLSASVGDRVTITCRSSQSLVHSNGNTFLHWYQQKPGKAPKLLIYTVSNRF
SGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCSQTTHVPWTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, D, J, K), FASTA

>8YX9_3 Tumor necrosis factor receptor superfamily member 5 (chains A, D, J, K)
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
8YX1 2.7 Å, CD40 in complex with Bleselumab Fab
5DMJ 2.79 Å, Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB
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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