6PE8: CD40/ABBV-323 FAB complex

Crystal structure of CD40/ABBV-323 FAB complex. Determined by X-ray diffraction at 2.84 Å resolution. Released 14 Aug 2019.

Method: X-ray diffraction
Resolution: 2.84 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,151
Mol. weight: 134.84 kDa
Released: 14 Aug 2019

Explore 6PE8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PE8 contains 55 α-helices and 131 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: 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
α-helix	121-122	2
β-strand	123-127	5	4
β-strand	138-148	11	4
β-strand	149	1	3
β-strand	154-157	4	5
α-helix	158-160	3
β-strand	162	1	5
β-strand	167-168	2	4
α-helix	169-171	3
β-strand	172-173	2	4
β-strand	179-188	10	4
β-strand	197-203	7	5
α-helix	204-206	3
β-strand	208-214	7	5
α-helix	216-218	3

Chain B: 9 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	108-113	6	7
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	150-156	7	11
β-strand	159-160	2	11
α-helix	161	1
β-strand	165-169	5	10
α-helix	170-173	4
β-strand	179-188	10	10
α-helix	189-194	6
β-strand	197-204	8	11
β-strand	211-216	6	11

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	103-106	4	13
β-strand	110-114	5	13
β-strand	120	1	14
α-helix	121-122	2
β-strand	123-127	5	15
β-strand	140-148	9	15
β-strand	149	1	14
β-strand	154-157	4	5
α-helix	158-160	3
β-strand	167-168	2	15
α-helix	169-171	3
β-strand	172-173	2	15
β-strand	179-186	8	15
α-helix	189-193	5
β-strand	197-203	7	5
α-helix	204-206	3
β-strand	208-214	7	5

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
α-helix	18	1
β-strand	19-25	7	16
β-strand	30	1	18
β-strand	37	1	18
β-strand	39-44	6	17
β-strand	51-55	5	17
β-strand	59-60	2	17
α-helix	61	1
β-strand	68-73	6	16
β-strand	76-81	6	16
α-helix	86-88	3
β-strand	91-96	6	17
β-strand	104	1	17
β-strand	108-113	6	17
β-strand	117	1	19
α-helix	118-119	2
β-strand	120-124	5	20
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	20
β-strand	146	1	19
β-strand	150-156	7	21
β-strand	159-160	2	21
α-helix	161	1
β-strand	165-169	5	20
α-helix	170-173	4
β-strand	179-188	10	20
α-helix	189-193	5
β-strand	197-204	8	21
β-strand	211-216	6	21

Chain T: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	30-33	4	22
β-strand	36-39	4	22
α-helix	40	1
β-strand	41	1	23
α-helix	42	1
β-strand	45-49	5	24
α-helix	56-57	2
β-strand	58-61	4	24
α-helix	62-63	2
β-strand	66-67	2	25
β-strand	72	1	23
β-strand	78-79	2	25
α-helix	80-81	2
α-helix	85-87	3
β-strand	89-93	5	26
β-strand	102-105	4	26
β-strand	110-111	2	27
β-strand	119-120	2	27
β-strand	125	1	28
β-strand	129-133	5	29
α-helix	140-141	2
β-strand	142-145	4	29
β-strand	150-151	2	30
β-strand	156	1	28
α-helix	159-161	3
β-strand	162-163	2	30
α-helix	164-166	3
β-strand	172	1	31
α-helix	183-184	2
β-strand	185	1	31

Chain U: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	32
β-strand	36-39	4	32
α-helix	40	1
β-strand	41	1	33
α-helix	42	1
β-strand	45-49	5	34
β-strand	58-61	4	34
β-strand	66-67	2	35
β-strand	72	1	33
α-helix	77	1
β-strand	78-79	2	35
α-helix	80-82	3
α-helix	85-87	3
β-strand	89-93	5	36
β-strand	96	1	37
β-strand	99	1	37
α-helix	100-101	2
β-strand	102-105	4	36
β-strand	110-111	2	38
β-strand	119-120	2	38
β-strand	125	1	39
β-strand	129-133	5	40
β-strand	136	1	41
β-strand	139	1	41
α-helix	140-141	2
β-strand	142-145	4	40
β-strand	150-151	2	42
β-strand	156	1	39
α-helix	159-161	3
β-strand	162-163	2	42
α-helix	164-165	2
α-helix	183-185	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FAB Heavy chain	A, H	protein	223	Homo sapiens
FAB Light chain	B, L	protein	220	Homo sapiens
Tumor necrosis factor receptor superfamily member 5	T, U	protein	173	Homo sapiens	P25942 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>6PE8_1 FAB Heavy chain (chains A, H)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSDYGMNWVRQAPGKGLEWIAYISSGRGNIYY
ADTVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARSWGYFDVWGQGTTVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (B, L), FASTA

>6PE8_2 FAB Light chain (chains B, L)
DIVMTQSPDSLAVSLGERATINCKSSQSLLNRGNQKNYLTWFQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQNDYTYPLTFGQGTKLEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (T, U), FASTA

>6PE8_3 Tumor necrosis factor receptor superfamily member 5 (chains T, U)
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
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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