4N90: PDB entry 4N90

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody. Determined by X-ray diffraction at 3.3 Å resolution. Released 3 Sept 2014.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 12
Atoms: 15,934
Mol. weight: 242.78 kDa
Ligands: ZN
Released: 3 Sept 2014

Explore 4N90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N90 contains 51 α-helices and 210 β-strands across 12 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	20
α-helix	132-134	3
β-strand	149-150	2	21
β-strand	154-155	2	20
β-strand	163-165	3	20
β-strand	167-169	3	21
β-strand	173-176	4	21
β-strand	180-192	13	20
β-strand	205-213	9	21
β-strand	220-228	9	21
α-helix	229-230	2
β-strand	238-250	13	20
β-strand	255-260	6	21
α-helix	263-265	3
β-strand	266-267	2	20
β-strand	274-280	7	20

Chain B: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	123-127	5	21
β-strand	128	1	22
α-helix	132-134	3
β-strand	149-150	2	23
β-strand	154	1	22
β-strand	163-165	3	21
β-strand	167-170	4	23
β-strand	173-176	4	23
β-strand	180-193	14	21
β-strand	205-214	10	23
β-strand	216-228	13	23
β-strand	237-250	14	21
β-strand	255-260	6	23
α-helix	263-265	3
β-strand	266	1	21
β-strand	274-279	6	21

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	23
β-strand	149-150	2	20
β-strand	154-155	2	23
β-strand	164-165	2	23
β-strand	167-169	3	20
β-strand	173-176	4	20
β-strand	180-193	14	23
β-strand	205-213	9	20
β-strand	220-228	9	20
β-strand	237-250	14	23
β-strand	255-260	6	20
α-helix	263-265	3
β-strand	266-267	2	23
β-strand	274-279	6	23

Chain D: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	11-12	2	30
β-strand	18-25	8	29
β-strand	35-41	7	31
β-strand	47-54	8	31
β-strand	59-61	3	31
β-strand	69-74	6	29
α-helix	75-77	3
β-strand	79-84	6	29
α-helix	89-91	3
β-strand	93-101	9	31
β-strand	108-112	5	31
β-strand	116-118	3	31
β-strand	119-120	2	30
β-strand	126	1	32
α-helix	127-128	2
β-strand	129-133	5	33
β-strand	144-154	11	33
β-strand	155	1	32
β-strand	160-163	4	34
β-strand	168	1	34
β-strand	173-174	2	33
β-strand	178-179	2	33
β-strand	185-194	10	33
α-helix	195-197	3
β-strand	198	1	35
β-strand	201	1	35
β-strand	203-209	7	34
α-helix	210-212	3
β-strand	214-220	7	34

Chain E: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-29	11	24
β-strand	34-39	6	25
α-helix	44-45	2
β-strand	46-50	5	25
β-strand	54-55	2	25
α-helix	56	1
β-strand	63-76	14	24
α-helix	81-83	3
β-strand	85-91	7	25
β-strand	98-99	2	25
β-strand	103-107	5	25
α-helix	108	1
β-strand	112	1	26
β-strand	115-119	5	27
α-helix	123-127	5
β-strand	131-140	10	27
β-strand	141	1	26
β-strand	146-151	6	28
β-strand	154-155	2	28
α-helix	156	1
β-strand	160-164	5	27
α-helix	165-168	4
β-strand	174-182	9	27
α-helix	184-189	6
β-strand	192-198	7	28
β-strand	206-211	6	28

Chain F: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	40
β-strand	11-12	2	41
β-strand	18-25	8	40
β-strand	35-41	7	37
β-strand	47-53	7	37
β-strand	59-61	3	37
β-strand	69-74	6	40
α-helix	75-77	3
β-strand	79-84	6	40
α-helix	89-91	3
β-strand	93-100	8	37
β-strand	109-112	4	37
β-strand	116-118	3	37
β-strand	119-120	2	41
β-strand	129-132	4	42
β-strand	145-146	2	43
β-strand	149-154	6	42
β-strand	162-163	2	44
β-strand	172-174	3	45
α-helix	175-177	3
β-strand	178-179	2	42
β-strand	185-187	3	42
β-strand	189-191	3	45
β-strand	192-193	2	43
α-helix	195-197	3
β-strand	204-208	5	44
β-strand	215-219	5	44

Chain G: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-13	4	37
β-strand	19-29	11	36
β-strand	34-39	6	37
β-strand	46-50	5	37
β-strand	54-55	2	37
α-helix	56	1
β-strand	63-76	14	36
β-strand	86-91	6	37
β-strand	98-99	2	37
β-strand	100	1	36
β-strand	103-107	5	37
α-helix	108	1
β-strand	119	1	38
α-helix	125-128	4
β-strand	132-140	9	38
β-strand	146-151	6	39
β-strand	160-161	2	38
β-strand	164	1	38
α-helix	165-168	4
β-strand	174-181	8	38
α-helix	184-187	4
β-strand	193-198	6	39
β-strand	206-210	5	39

Chain H: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	50
β-strand	11-12	2	51
β-strand	19-25	7	50
β-strand	35-41	7	52
β-strand	47-53	7	52
β-strand	59-61	3	52
β-strand	70-74	5	50
β-strand	79-83	5	50
α-helix	89-91	3
β-strand	93-100	8	52
β-strand	109-112	4	52
β-strand	116-118	3	52
β-strand	119-120	2	51
β-strand	126	1	53
α-helix	127-128	2
β-strand	129-133	5	54
β-strand	144-152	9	54
β-strand	154	1	55
β-strand	155	1	53
β-strand	160-163	4	56
β-strand	173-174	2	54
β-strand	178-179	2	55
β-strand	185-186	2	55
β-strand	188-194	7	54
α-helix	195-197	3
β-strand	203-209	7	56
α-helix	210-212	3
β-strand	214-220	7	56

4 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
Tumor necrosis factor receptor superfamily member 10B	R, S, T	protein	126	Homo sapiens	O14763 (AlphaFold model)
Tumor necrosis factor ligand superfamily member 10	A, B, C	protein	168	Homo sapiens	P50591 (AlphaFold model)
Fab light chain	E, G, I	protein	215	Homo sapiens
Fab heavy chain	D, F, H	protein	224	Homo sapiens

Sequence of entity 1 (R, S, T), FASTA

>4N90_1 Tumor necrosis factor receptor superfamily member 10B (chains R, S, T)
TQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRC
TRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDI
ECVHKE

Sequence of entity 2 (A, B, C), FASTA

>4N90_2 Tumor necrosis factor ligand superfamily member 10 (chains A, B, C)
VRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGE
LVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSK
DAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Sequence of entity 3 (E, G, I), FASTA

>4N90_3 Fab light chain (chains E, G, I)
EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D, F, H), FASTA

>4N90_4 Fab heavy chain (chains D, F, H)
QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTY
YNPSLKSRVTISVDTSKKQFSLRLSSVTAADTAVYYCARDRGGDYYYGMDVWGQGTTVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Apo2L/TRAIL and the Death Receptor 5 Agonist Antibody AMG 655 Cooperate to Promote Receptor Clustering and Antitumor Activity. Graves, J.D., Kordich, J.J., Huang, T.H. et al. Cancer Cell (2014) 26:177-189. DOI 10.1016/j.ccr.2014.04.028 · 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
6T3J 3.05 Å, Dual Epitope Targeting by Anti-DR5 Antibodies
4OD2 3.2 Å, Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5
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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