6PE9: CD40 complexed to FAB516

Crystal Structure of CD40 complexed to FAB516. Determined by X-ray diffraction at 3.13 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 3.13 Å
Organism: Homo sapiens
Chains: 15
Atoms: 18,618
Mol. weight: 336.56 kDa
Released: 14 Aug 2019

Explore 6PE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PE9 contains 89 α-helices and 275 β-strands across 15 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	103-106	4	2
β-strand	110-114	5	2
β-strand	120	1	3
β-strand	123-127	5	4
β-strand	138-148	11	4
β-strand	149	1	3
β-strand	153-157	5	5
α-helix	158-160	3
β-strand	162	1	5
β-strand	166-168	3	4
α-helix	169-171	3
β-strand	172-173	2	4
β-strand	179-188	10	4
α-helix	189-191	3
β-strand	199-203	5	5
α-helix	204-206	3
β-strand	208-212	5	5
α-helix	216-218	3

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	30-31	2	8
β-strand	36-37	2	8
β-strand	39-44	6	7
β-strand	51-55	5	7
β-strand	59-60	2	7
α-helix	61	1
β-strand	68-73	6	6
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	90-96	7	7
α-helix	102	1
β-strand	104	1	7
β-strand	109-113	5	7
β-strand	117	1	9
β-strand	120-124	5	10
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	150-156	7	11
β-strand	159-160	2	11
β-strand	165-169	5	10
α-helix	170-173	4
β-strand	179-188	10	10
α-helix	189-193	5
β-strand	197-204	8	11
β-strand	211-216	6	11

Chain C: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	17-25	9	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	46-51	6	14
β-strand	58-60	3	14
β-strand	68-73	6	12
β-strand	78-84	7	12
α-helix	88-90	3
β-strand	92-100	9	14
β-strand	102-106	5	14
β-strand	110-112	3	14
β-strand	113-114	2	13
β-strand	120	1	15
α-helix	121-122	2
β-strand	123-127	5	16
β-strand	138-148	11	16
β-strand	149	1	15
β-strand	154-157	4	17
β-strand	166-168	3	16
α-helix	169-171	3
β-strand	172-173	2	16
β-strand	179-188	10	16
β-strand	197-198	2	18
β-strand	199-203	5	17
α-helix	204-206	3
β-strand	208-210	3	17
α-helix	212	1
β-strand	213-214	2	18

Chain D: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-14	5	20
β-strand	19-25	7	19
β-strand	30-31	2	21
β-strand	36-37	2	21
β-strand	39-44	6	20
α-helix	49-50	2
β-strand	51-55	5	20
β-strand	59-60	2	20
α-helix	61	1
β-strand	68-73	6	19
β-strand	76-81	6	19
α-helix	86-88	3
β-strand	90-96	7	20
α-helix	102	1
β-strand	103-104	2	20
β-strand	108-113	6	20
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	23
α-helix	125-127	3
α-helix	129-133	5
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	150-151	2	24
β-strand	154-156	3	25
β-strand	160	1	25
β-strand	165-169	5	23
β-strand	179-188	10	23
α-helix	189-192	4
β-strand	197-202	6	25
β-strand	203-204	2	24
β-strand	211-216	6	25

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	10-12	3	27
β-strand	18-25	8	26
β-strand	33-39	7	27
β-strand	45-51	7	27
β-strand	58-60	3	27
β-strand	65	1	28
β-strand	68	1	28
β-strand	69-73	5	26
β-strand	78-83	6	26
α-helix	88-90	3
β-strand	92-99	8	27
β-strand	103-106	4	27
β-strand	110-114	5	27
β-strand	120	1	29
β-strand	123-127	5	30
α-helix	128-129	2
β-strand	138-148	11	30
β-strand	149	1	29
β-strand	154-157	4	31
α-helix	158-160	3
β-strand	162	1	31
β-strand	166-168	3	30
α-helix	169-171	3
β-strand	172-174	3	30
β-strand	178-188	11	30
β-strand	198-203	6	31
α-helix	204-206	3
β-strand	208-213	6	31

Chain F: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	32
β-strand	10-14	5	33
β-strand	19-25	7	32
β-strand	30-31	2	34
β-strand	36-37	2	34
β-strand	39-44	6	33
α-helix	49-50	2
β-strand	51-55	5	33
β-strand	59-60	2	33
α-helix	61	1
β-strand	68-73	6	32
β-strand	76-81	6	32
α-helix	86-88	3
β-strand	90-96	7	33
α-helix	102	1
β-strand	103-104	2	33
β-strand	109-113	5	33
β-strand	117	1	35
β-strand	122-123	2	36
α-helix	125-127	3
α-helix	130-132	3
β-strand	135-139	5	37
β-strand	140-141	2	36
β-strand	142-145	4	38
β-strand	146	1	35
β-strand	151-156	6	39
β-strand	159-160	2	39
β-strand	165-166	2	37
β-strand	169	1	38
β-strand	179-181	3	38
β-strand	184-188	5	37
α-helix	189-193	5
β-strand	197-203	7	39
β-strand	211-212	2	39
β-strand	215-216	2	39

Chain G: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	40
β-strand	36-39	4	40
α-helix	40	1
β-strand	41	1	41
α-helix	42	1
β-strand	45-49	5	42
α-helix	55-57	3
β-strand	58-61	4	42
β-strand	66-67	2	43
β-strand	72	1	41
α-helix	77	1
β-strand	78-79	2	43
α-helix	80-81	2
α-helix	85-87	3
β-strand	89-93	5	44
β-strand	102-105	4	44
α-helix	106	1
β-strand	109-111	3	45
β-strand	119-121	3	45
α-helix	122-124	3
β-strand	130-131	2	46
β-strand	136	1	47
β-strand	139	1	47
α-helix	140-142	3
β-strand	143-144	2	46

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	48
β-strand	10-12	3	49
β-strand	17-25	9	48
α-helix	29-31	3
β-strand	33-39	7	49
β-strand	46-51	6	49
β-strand	58-60	3	49
α-helix	62-64	3
β-strand	68-73	6	48
β-strand	78-84	7	48
α-helix	88-90	3
β-strand	92-99	8	49
β-strand	103-106	4	49
β-strand	110-114	5	49
α-helix	118-119	2
β-strand	120	1	50
β-strand	123-127	5	51
β-strand	138-148	11	51
β-strand	149	1	50
β-strand	154-157	4	52
α-helix	158-160	3
β-strand	162	1	52
β-strand	166-168	3	51
α-helix	169-171	3
β-strand	172-173	2	51
β-strand	179-188	10	51
α-helix	189-192	4
β-strand	197-203	7	52
α-helix	204-206	3
β-strand	208-214	7	52
α-helix	216-218	3

7 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
FAB Heavy chain	A, C, E, H, K	protein	223	Homo sapiens
FAB Light chain	B, D, F, L, M	protein	220	Homo sapiens
Tumor necrosis factor receptor superfamily member 5	G, I, J, U, V	protein	173	Homo sapiens	P25942 (AlphaFold model)

Sequence of entity 1 (A, C, E, H, K), FASTA

>6PE9_1 FAB Heavy chain (chains A, C, E, H, K)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSDYGMNWVRQAPGKGLEWVSYISSGRSNIYY
ADTVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARSWGYFDVWGQGTTVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (B, D, F, L, M), FASTA

>6PE9_2 FAB Light chain (chains B, D, F, L, M)
DIVMTQSPDSLAVSLGERATINCKSSQSLLNLGNQKNYLTWFQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQNDYTYPLTFGQGTKLEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (G, I, J, U, V), FASTA

>6PE9_3 Tumor necrosis factor receptor superfamily member 5 (chains G, I, J, U, V)
EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQH
KYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSD
TICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDRLR

Primary citation

CD40/anti-CD40 antibody complexes which illustrate agonist and antagonist structural switches. Argiriadi, M.A., Benatuil, L., Dubrovska, I. et al. BMC Mol Cell Biol (2019) 20:29-29. DOI 10.1186/s12860-019-0213-4 · 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
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
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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