6T3J: Dual Epitope Targeting by Anti-DR5 Antibodies

Dual Epitope Targeting by Anti-DR5 Antibodies. Determined by X-ray diffraction at 3.05 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 10
Atoms: 14,837
Mol. weight: 223.38 kDa
Released: 16 Sept 2020

Explore 6T3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T3J contains 71 α-helices and 200 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
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	45-52	8	2
β-strand	57-60	4	2
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	101	1	3
β-strand	107-108	2	2
β-strand	112-116	5	2
β-strand	122	1	4
β-strand	125-129	5	5
α-helix	130-132	3
β-strand	141-150	10	5
β-strand	151	1	4
β-strand	156-159	4	6
β-strand	168-170	3	5
α-helix	171-173	3
β-strand	174-175	2	5
β-strand	181-189	9	5
α-helix	191-193	3
β-strand	199-205	7	6
α-helix	206-208	3
β-strand	210-216	7	6

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	154	1	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	192-198	7	11
β-strand	205-209	5	11

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-52	8	13
β-strand	57-60	4	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-100	9	13
β-strand	103-108	6	13
β-strand	112-116	5	13
α-helix	119-121	3
β-strand	122	1	14
β-strand	125-129	5	15
α-helix	130-132	3
β-strand	140-150	11	15
β-strand	151	1	14
β-strand	156-159	4	16
β-strand	168-170	3	15
α-helix	171-173	3
β-strand	174-175	2	15
β-strand	181-190	10	15
α-helix	191-193	3
β-strand	199-205	7	16
α-helix	206-208	3
β-strand	210-216	7	16

Chains D and I: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-13	4	18
β-strand	19-25	7	17
β-strand	33-37	5	18
α-helix	42-43	2
β-strand	44-48	5	18
β-strand	52-53	2	18
α-helix	54	1
β-strand	61-65	5	17
β-strand	69-74	6	17
α-helix	79-81	3
β-strand	84-89	6	18
α-helix	95	1
β-strand	96-97	2	18
β-strand	101-105	5	18
β-strand	110	1	19
β-strand	113-117	5	20
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	20
β-strand	139	1	19
β-strand	143-149	7	21
β-strand	153	1	21
β-strand	158-162	5	20
α-helix	163-166	4
β-strand	172-181	10	20
α-helix	182-187	6
β-strand	190-197	8	21
β-strand	204-209	6	21

Chain E: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	81	1	22
α-helix	82	1
β-strand	85-87	3	23
β-strand	94-96	3	23
α-helix	97-98	2
β-strand	102-103	2	24
β-strand	108	1	22
β-strand	110	1	13
α-helix	113	1
β-strand	114-115	2	24
α-helix	116-117	2
β-strand	124-127	4	25
β-strand	136-138	3	25
β-strand	143-146	4	3
β-strand	152-155	4	3
α-helix	156-157	2
α-helix	160-161	2
β-strand	164-168	5	26
β-strand	171	1	27
β-strand	174	1	27
α-helix	175-176	2
β-strand	177-180	4	26

Chain F: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	28
α-helix	7-9	3
β-strand	10-12	3	29
β-strand	18-25	8	28
α-helix	29-31	3
β-strand	33-39	7	29
β-strand	45-52	8	29
β-strand	57-60	4	29
β-strand	68-73	6	28
β-strand	78-83	6	28
α-helix	88-90	3
β-strand	92-99	8	29
β-strand	101	1	30
β-strand	107-108	2	29
β-strand	112-116	5	29
β-strand	122	1	31
β-strand	125-129	5	32
β-strand	140-150	11	32
β-strand	151	1	31
β-strand	156-159	4	33
β-strand	168-170	3	32
α-helix	171-173	3
β-strand	174-175	2	32
β-strand	181-190	10	32
α-helix	191-193	3
β-strand	199-205	7	33
α-helix	206-208	3
β-strand	210-216	7	33

Chain G: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	34
β-strand	10-13	4	29
β-strand	19-25	7	34
β-strand	33-38	6	29
β-strand	45-49	5	29
β-strand	53-54	2	29
β-strand	62-67	6	34
β-strand	70-75	6	34
α-helix	80-82	3
β-strand	85-90	6	29
α-helix	96	1
β-strand	97-98	2	29
β-strand	102-106	5	29
β-strand	111	1	35
β-strand	114-118	5	36
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	36
β-strand	140	1	35
β-strand	145-150	6	37
β-strand	154	1	37
β-strand	159-163	5	36
α-helix	164-167	4
β-strand	173-182	10	36
α-helix	183-188	6
β-strand	191-197	7	37
β-strand	205-210	6	37

Chain H: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	38
α-helix	7-9	3
β-strand	10-12	3	39
β-strand	18-25	8	38
α-helix	29-31	3
β-strand	34-39	6	39
β-strand	45-52	8	39
β-strand	57-60	4	39
β-strand	68-73	6	38
β-strand	78-83	6	38
α-helix	88-90	3
β-strand	92-100	9	39
β-strand	103-108	6	39
β-strand	112-116	5	39
β-strand	122	1	40
β-strand	125-129	5	41
α-helix	130-132	3
β-strand	140-150	11	41
β-strand	151	1	40
β-strand	156-159	4	42
β-strand	168-170	3	41
α-helix	171-173	3
β-strand	174-175	2	41
β-strand	181-190	10	41
α-helix	191-193	3
β-strand	199-205	7	42
α-helix	206-208	3
β-strand	210-216	7	42

1 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
IgG1-hDR5-01-Heavy Chain	A, F	protein	232	Homo sapiens
IgG1-hDR5-01-Light Chain	B, G	protein	214	Homo sapiens
IgG1-hDR5-05-Heavy Chain	C, H	protein	232	Homo sapiens
IgG1-hDR5-05-Light Chain	D, I	protein	213	Homo sapiens
Tumor necrosis factor receptor superfamily member 10B	E, J	protein	131	Homo sapiens	O14763 (AlphaFold model)

Sequence of entity 1 (A, F), FASTA

>6T3J_1 IgG1-hDR5-01-Heavy Chain (chains A, F)
EVQLQQSGAEVVKPGASVKLSCKASGFNIKDTFIHWVKQAPGQGLEWIGRIDPANTNTKY
DPKFQGKATITTDTSSNTAYMELSSLRSEDTAVYYCVRGLYTYYFDYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTHHHHHH

Sequence of entity 2 (B, G), FASTA

>6T3J_2 IgG1-hDR5-01-Light Chain (chains B, G)
EIVMTQSPATLSVSPGERATLSCRASQSISNNLHWYQQKPGQAPRLLIKFASQSITGIPA
RFSGSGSGTEFTLTISSLQSEDFAVYYCQQGNSWPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, H), FASTA

>6T3J_3 IgG1-hDR5-05-Heavy Chain (chains C, H)
QVQLVQSGAEVKKPGASVKVSCKASGFNIKDTHMHWVRQAPGQRLEWIGRIDPANGNTEY
DQKFQGRVTITVDTSASTAYMELSSLRSEDTAVYYCARWGTNVYFAYWGQGTLVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTHHHHHH

Sequence of entity 4 (D, I), FASTA

>6T3J_4 IgG1-hDR5-05-Light Chain (chains D, I)
DIQLTQSPSSLSASVGDRVTITCSASSSVSYMYWYQQKPGKAPKPWIYRTSNLASGVPSR
FSGSGSGTDFTLTISSLQPEDFATYYCQQYHSYPPTFGGGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (E, J), FASTA

>6T3J_5 Tumor necrosis factor receptor superfamily member 10B (chains E, J)
QQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCT
RCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIE
CVHKESGEPEA

Primary citation

Dual Epitope Targeting and Enhanced Hexamerization by DR5 Antibodies as a Novel Approach to Induce Potent Antitumor Activity Through DR5 Agonism. Overdijk, M.B., Strumane, K., Beurskens, F.J. et al. Mol Cancer Ther (2020) 19:2126-2138. DOI 10.1158/1535-7163.MCT-20-0044 · PubMed

Other PDB entries of the same protein (UniProt O14763 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3X3F 2.1 Å, TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody…
4I9X 2.1 Å, Crystal structure of human cytomegalovirus glycoprotein UL141 targeting the death…
1D4V 2.2 Å, Crystal structure of trail-DR5 complex
1DU3 2.2 Å, Crystal structure of TRAIL-SDR5
2H9G 2.32 Å, Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5)
1D0G 2.4 Å, Crystal structure of death receptor 5 (DR5) bound to APO2L/TRAIL
4OD2 3.2 Å, Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5
4N90 3.3 Å, Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist…
1ZA3 3.35 Å, The crystal structure of the YSd1 Fab bound to DR5
6NHW Structure of the transmembrane domain of the Death Receptor 5 - Dimer of Trimer
6NHY Structure of the transmembrane domain of the Death Receptor 5 mutant (G217Y) - Trimer Only
8DPX Preligand association structure of DR5

Browse structure collections

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