3QD6: CD40 and CD154 (CD40L) complex

Crystal structure of the CD40 and CD154 (CD40L) complex. Determined by X-ray diffraction at 3.5 Å resolution. Released 2 Feb 2011.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 10
Atoms: 9,896
Mol. weight: 176.02 kDa
Ligands: NAG
Released: 2 Feb 2011

Explore 3QD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QD6 contains 31 α-helices and 144 β-strands across 10 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: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	1
β-strand	137	1	2
α-helix	138-139	2
β-strand	140-141	2	1
β-strand	147-148	2	1
β-strand	153-156	4	3
β-strand	160-163	4	3
β-strand	167-178	12	1
β-strand	190-192	3	2
β-strand	195-196	2	3
β-strand	207-209	3	2
α-helix	211-213	3
β-strand	220-231	12	1
β-strand	236-237	2	3
β-strand	240-241	2	2
β-strand	247	1	1
β-strand	255-260	6	1

Chain B: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	4
β-strand	137	1	5
β-strand	139-141	3	4
β-strand	147-148	2	4
β-strand	153-154	2	6
α-helix	156-158	3
β-strand	161-163	3	6
β-strand	167-178	12	4
β-strand	190-192	3	5
β-strand	195-196	2	6
β-strand	207-209	3	5
β-strand	220-231	12	4
β-strand	236-237	2	6
β-strand	240	1	5
β-strand	247	1	4
β-strand	255-260	6	4

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	7
β-strand	137	1	8
α-helix	138	1
β-strand	139-141	3	7
β-strand	147-148	2	7
β-strand	153-154	2	9
α-helix	156-158	3
β-strand	161-163	3	9
β-strand	167-178	12	7
β-strand	191-192	2	8
β-strand	195-196	2	9
β-strand	207-208	2	8
β-strand	220-231	12	7
β-strand	236-237	2	9
β-strand	240	1	8
β-strand	255-260	6	7

Chain D: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	10
β-strand	137	1	11
α-helix	138	1
β-strand	139-141	3	10
β-strand	147-148	2	10
β-strand	153-154	2	12
α-helix	156-158	3
β-strand	161-163	3	12
β-strand	167-176	10	10
β-strand	177	1	13
β-strand	190-192	3	11
β-strand	195-196	2	12
β-strand	207-209	3	11
β-strand	210	1	14
β-strand	221	1	15
β-strand	222-231	10	10
β-strand	236-237	2	12
β-strand	240	1	11
β-strand	247	1	13
β-strand	255-260	6	10

Chain E: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-129	7	16
β-strand	137	1	15
α-helix	138	1
β-strand	139-141	3	16
β-strand	147-148	2	16
β-strand	153-154	2	17
α-helix	156-158	3
β-strand	161-163	3	17
β-strand	167-178	12	16
β-strand	189-192	4	15
β-strand	195-196	2	17
β-strand	207-210	4	15
α-helix	211-213	3
β-strand	220-231	12	16
β-strand	236-237	2	17
β-strand	240	1	15
β-strand	247	1	16
β-strand	255-260	6	16

Chain F: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	14
β-strand	137	1	18
α-helix	138-139	2
β-strand	140-141	2	14
β-strand	147-148	2	14
β-strand	153-154	2	19
α-helix	156-158	3
β-strand	161-163	3	19
β-strand	167-178	12	14
β-strand	191-192	2	18
β-strand	195-196	2	19
β-strand	207-208	2	18
β-strand	210	1	16
β-strand	220-231	12	14
β-strand	236-237	2	19
β-strand	240-241	2	18
β-strand	255-260	6	14

Chain R: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	20
β-strand	37-38	2	20
β-strand	41	1	21
β-strand	45	1	22
β-strand	49	1	23
β-strand	58	1	23
β-strand	61	1	22
β-strand	66-67	2	24
β-strand	72	1	21
β-strand	78-79	2	24
α-helix	80-81	2
α-helix	85-87	3
β-strand	89-93	5	25
β-strand	102-105	4	25
α-helix	106	1
β-strand	109-111	3	26
β-strand	119-121	3	26

Chain S: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	30-32	3	27
β-strand	37-39	3	27
α-helix	40	1
β-strand	41	1	28
α-helix	42	1
β-strand	45-49	5	29
α-helix	56-57	2
β-strand	58-61	4	29
β-strand	66-67	2	30
β-strand	72	1	28
β-strand	78-79	2	30
α-helix	80-81	2
α-helix	85-87	3
β-strand	89-93	5	31
β-strand	102-105	4	31
α-helix	106	1
β-strand	111	1	32
β-strand	119	1	32

2 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
CD40 ligand	A, B, C, D, E, F	protein	149	Homo sapiens	P29965 (AlphaFold model)
Tumor necrosis factor receptor superfamily member 5	R, S, T, U	protein	177	Homo sapiens	P25942 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>3QD6_1 CD40 ligand (chains A, B, C, D, E, F)
ADPGDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIY
AQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQ
PGASVFVNVTDPSQVSHGTGFTSFGLLKL

Sequence of entity 2 (R, S, T, U), FASTA

>3QD6_2 Tumor necrosis factor receptor superfamily member 5 (chains R, S, T, U)
EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQH
KYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSD
TICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDSGRLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Crystallographic and mutational analysis of the CD40-CD154 complex and its implications for receptor activation. An, H.-J., Kim, Y.J., Song, D.H. et al. J Biol Chem (2011) 286:11226-11235. DOI 10.1074/jbc.M110.208215 · PubMed

Other PDB entries of the same protein (UniProt P29965 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W9G 1.82 Å, Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the…
1ALY 2.0 Å, Crystal structure of human CD40 ligand
7SGM 2.0 Å, Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with…
3LKJ 2.5 Å, Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit…
6BRB 2.82 Å, Novel non-antibody protein scaffold targeting CD40L
1I9R 3.1 Å, Structure of CD40L in complex with the FAB fragment of humanized 5C8 antibody
9I5N 3.4 Å, Single particle cryo electron microscopy of a Fab fragment bound to recombinant human…

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