5DMJ: Extracellular domain of the CD40

Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB. Determined by X-ray diffraction at 2.79 Å resolution. Released 1 Jun 2016.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,160
Mol. weight: 100.19 kDa
Released: 1 Jun 2016

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

Secondary structure: helices and β-sheets

5DMJ contains 38 α-helices and 101 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	1
β-strand	37	1	1
α-helix	38-40	3
β-strand	41	1	2
α-helix	42	1
β-strand	45-49	5	3
α-helix	56-57	2
β-strand	58-61	4	3
α-helix	62-63	2
β-strand	66-67	2	4
β-strand	72	1	2
α-helix	77	1
β-strand	78-79	2	4
α-helix	80-82	3
α-helix	85-87	3
β-strand	89-93	5	5
α-helix	100-101	2
β-strand	102-105	4	5
β-strand	110-111	2	6
β-strand	119-120	2	6
β-strand	125	1	7
β-strand	130-131	2	8
β-strand	136	1	9
β-strand	139	1	9
α-helix	140-142	3
β-strand	143-144	2	8
β-strand	150-151	2	10
β-strand	156	1	7
α-helix	159-161	3
β-strand	162-163	2	10
α-helix	164	1
β-strand	175-176	2	11
β-strand	185	1	11

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	14
α-helix	44	1
β-strand	45-51	7	14
β-strand	57-59	3	14
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-94	7	14
β-strand	98	1	6
β-strand	103	1	14
β-strand	107-109	3	14
β-strand	110-111	2	13

Chain D: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	15
β-strand	37	1	15
α-helix	39-40	2
β-strand	41	1	16
α-helix	42	1
β-strand	45-49	5	17
β-strand	58-61	4	17
α-helix	62-63	2
β-strand	66-67	2	18
β-strand	72	1	16
α-helix	77	1
β-strand	78-79	2	18
α-helix	80	1
α-helix	85-87	3
β-strand	89-93	5	19
β-strand	102-105	4	19
β-strand	110-111	2	20
β-strand	119-120	2	20
β-strand	125	1	21
β-strand	127	1	22
β-strand	129	1	22
β-strand	130-134	5	23
β-strand	141-144	4	23
α-helix	145-147	3
β-strand	150-151	2	24
β-strand	156	1	21
β-strand	162-163	2	24
α-helix	164-165	2
β-strand	174-176	3	25
β-strand	185-186	2	25

Chains E and G: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	34-39	6	28
α-helix	44	1
β-strand	45-51	7	28
β-strand	57-59	3	28
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-94	7	28
β-strand	103	1	28
β-strand	107-109	3	28
β-strand	110-111	2	27

Chain F: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	33	1	29
β-strand	37	1	29
α-helix	38-40	3
β-strand	41	1	30
α-helix	42	1
β-strand	45-46	2	31
β-strand	60-61	2	31
α-helix	62-63	2
β-strand	66-67	2	32
β-strand	72	1	30
α-helix	77	1
β-strand	78-79	2	32
α-helix	80	1
α-helix	85-87	3
β-strand	89-93	5	33
α-helix	100-101	2
β-strand	102-105	4	33
β-strand	110-111	2	34
β-strand	119-120	2	34
β-strand	125	1	35
β-strand	127	1	36
β-strand	129	1	36
β-strand	130-131	2	37
β-strand	143-144	2	37
β-strand	150-151	2	38
β-strand	156	1	35
α-helix	159-161	3
β-strand	162-163	2	38
α-helix	164-166	3
α-helix	168-170	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 5	A, D, F	protein	183	Homo sapiens	P25942 (AlphaFold model)
3H65-5 domain antibody (dAb)	B, E, G	protein	121	Homo sapiens

Sequence of entity 1 (A, D, F), FASTA

>5DMJ_1 Tumor necrosis factor receptor superfamily member 5 (chains A, D, F)
PTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKY
CDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTI
CEPCPVGFFSDVSSAFEKCHPWTSCETKDLVVQQAGTDKTDVVCGPQDRLRDPGGGGGRL
VPR

Sequence of entity 2 (B, E, G), FASTA

>5DMJ_2 3H65-5 domain antibody (dAb) (chains B, E, G)
STEVQLLESGGGLVQPGGSLRLSCAASGFTFRDYEMWWVRQAPGKGLERVSAINPQGTRT
YYADSVMGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLPFTFDDWGQGTLVTVSSAA
A

Primary citation

Functional Antagonism of Human CD40 Achieved by Targeting a Unique Species-Specific Epitope. Yamniuk, A.P., Suri, A., Krystek, S.R. et al. J Mol Biol (2016) 428:2860-2879. DOI 10.1016/j.jmb.2016.05.014 · 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
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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