1D0G: Death receptor 5

Crystal structure of death receptor 5 (DR5) bound to APO2L/TRAIL. Determined by X-ray diffraction at 2.4 Å resolution. Released 22 Oct 1999.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,576
Mol. weight: 102.4 kDa
Ligands: ZN
Released: 22 Oct 1999

Explore 1D0G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1D0G contains 23 α-helices and 89 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: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-127	5	25
β-strand	149-150	2	26
β-strand	155	1	25
β-strand	157	1	27
β-strand	162	1	27
β-strand	163-165	3	25
β-strand	167-170	4	26
β-strand	173-176	4	26
β-strand	180-192	13	25
β-strand	205-213	9	26
β-strand	220-228	9	26
α-helix	229-230	2
β-strand	238-250	13	25
β-strand	255-260	6	26
α-helix	263-265	3
β-strand	266	1	25
β-strand	274-279	6	25

Chains B and D: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	123-128	6	26
β-strand	149-150	2	28
β-strand	154-155	2	26
α-helix	158-160	3
β-strand	163-165	3	26
β-strand	167-170	4	28
β-strand	173-176	4	28
β-strand	180-192	13	26
β-strand	205-213	9	28
β-strand	220-228	9	28
β-strand	238-250	13	26
β-strand	255-260	6	28
α-helix	263-265	3
β-strand	266-267	2	26
β-strand	274-279	6	26

Chain R: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	1
β-strand	27	1	1
β-strand	28	1	2
β-strand	32-34	3	3
β-strand	41-43	3	3
α-helix	44-45	2
β-strand	49-50	2	4
β-strand	55	1	2
α-helix	60	1
β-strand	61-62	2	4
α-helix	63-64	2
β-strand	70-74	5	5
β-strand	83-86	4	5
α-helix	87	1
β-strand	90-93	4	6
β-strand	96-102	7	6
α-helix	103-104	2
β-strand	112-115	4	7
β-strand	118	1	8
β-strand	121	1	8
β-strand	124-126	3	7

Chain S: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	9
β-strand	27	1	9
β-strand	28	1	10
β-strand	32-34	3	11
β-strand	41-43	3	11
α-helix	44-45	2
β-strand	49-50	2	12
β-strand	55	1	10
α-helix	60	1
β-strand	61-62	2	12
α-helix	63-64	2
β-strand	70-74	5	13
β-strand	83-86	4	13
α-helix	87	1
β-strand	90-93	4	14
β-strand	96-102	7	14
α-helix	103-104	2
α-helix	107-108	2
β-strand	111-115	5	15
β-strand	118	1	16
β-strand	121	1	16
β-strand	124-127	4	15

Chain T: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	17
β-strand	27	1	17
β-strand	28	1	18
β-strand	32-34	3	19
β-strand	41-43	3	19
α-helix	44-45	2
β-strand	49-50	2	20
β-strand	55	1	18
α-helix	60	1
β-strand	61-62	2	20
α-helix	63-64	2
α-helix	66-67	2
β-strand	70-74	5	21
β-strand	83-86	4	21
α-helix	87	1
β-strand	90-91	2	22
β-strand	101-102	2	22
α-helix	103-104	2
β-strand	111-115	5	23
β-strand	118	1	24
β-strand	121	1	24
β-strand	124-127	4	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Death receptor-5	R, S, T	protein	130	Homo sapiens	O14763 (AlphaFold model)
Apoptosis-2 ligand	A, B, D	protein	168	Homo sapiens	P50591 (AlphaFold model)

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

>1D0G_1 DEATH RECEPTOR-5 (chains R, S, T)
ALITQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFC
LRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPW
SDIECVHKES

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

>1D0G_2 APOPTOSIS-2 LIGAND (chains A, B, D)
VRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGE
LVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSK
DAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Triggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5. Hymowitz, S.G., Christinger, H.W., Fuh, G. et al. Mol Cell (1999) 4:563-571. DOI 10.1016/S1097-2765(00)80207-5 · 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)
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
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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