1DU3: TRAIL-SDR5

Crystal structure of TRAIL-SDR5. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Sept 2000.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 12
Atoms: 12,108
Mol. weight: 204.73 kDa
Ligands: ZN
Released: 27 Sept 2000

Explore 1DU3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DU3 contains 38 α-helices and 177 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: 4 helices, 12 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	1
β-strand	49-50	2	4
β-strand	55	1	2
α-helix	60	1
β-strand	61-62	2	4
α-helix	63-66	4
β-strand	70-74	5	5
β-strand	83-86	4	5
α-helix	87	1
β-strand	91-93	3	6
β-strand	96-101	6	6

Chain B: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	7
β-strand	32-34	3	8
β-strand	41-43	3	8
α-helix	44-45	2
β-strand	49-50	2	9
β-strand	55	1	7
α-helix	60	1
β-strand	61-62	2	9
α-helix	63	1
β-strand	64	1	10
α-helix	65-66	2
β-strand	70-74	5	11
β-strand	77	1	12
β-strand	80	1	12
β-strand	83-86	4	11
α-helix	87	1
β-strand	90-91	2	13
β-strand	101-102	2	13
α-helix	103-104	2
β-strand	111	1	14
β-strand	115	1	15
β-strand	118	1	16
β-strand	121	1	16
β-strand	124	1	15
β-strand	127	1	14

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	28	1	17
β-strand	30	1	18
β-strand	32-33	2	18
β-strand	42-43	2	18
α-helix	44	1
β-strand	55	1	17
α-helix	62-63	2
β-strand	64	1	19
β-strand	70-74	5	20
β-strand	77	1	21
β-strand	80	1	21
β-strand	83-86	4	20
β-strand	91	1	22
β-strand	101	1	22
β-strand	118	1	23
β-strand	121	1	23

Chain D: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	123-127	5	24
β-strand	128	1	25
α-helix	132-134	3
β-strand	149-150	2	26
β-strand	154	1	25
β-strand	163-165	3	24
β-strand	167-169	3	26
β-strand	174-176	3	26
β-strand	180-192	13	24
β-strand	205-213	9	26
α-helix	219	1
β-strand	220-228	9	26
β-strand	238-250	13	24
β-strand	255-260	6	26
α-helix	263-265	3
β-strand	266-267	2	24
β-strand	274-280	7	24

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-127	5	27
β-strand	128	1	28
β-strand	132	1	10
β-strand	149-150	2	29
α-helix	151	1
β-strand	154	1	28
β-strand	163-165	3	27
β-strand	168-169	2	29
β-strand	174-175	2	29
β-strand	180-192	13	27
β-strand	205-213	9	29
β-strand	220-228	9	29
β-strand	238-250	13	27
β-strand	255-260	6	29
α-helix	263-265	3
β-strand	266-267	2	27
β-strand	274-279	6	27

Chain F: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	123-127	5	29
β-strand	128	1	30
β-strand	132	1	19
β-strand	149-150	2	24
β-strand	154	1	30
β-strand	163-165	3	29
β-strand	167-169	3	24
β-strand	174-176	3	24
β-strand	180-192	13	29
β-strand	205-214	10	24
β-strand	216-228	13	24
β-strand	238-250	13	29
β-strand	255-260	6	24
α-helix	263-265	3
β-strand	266	1	29
β-strand	274-279	6	29

Chain G: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	31
α-helix	29	1
β-strand	32-34	3	32
β-strand	41-43	3	32
α-helix	44-45	2
β-strand	55	1	31
α-helix	60-66	7
β-strand	70-74	5	33
β-strand	77	1	34
β-strand	80	1	34
β-strand	83-86	4	33
α-helix	87	1
β-strand	90-91	2	35
β-strand	101-102	2	35
β-strand	111-115	5	36
β-strand	118	1	37
β-strand	121	1	37
α-helix	122-123	2
β-strand	124-127	4	36

Chain H: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	38
β-strand	32-34	3	39
β-strand	41-43	3	39
α-helix	44-45	2
β-strand	49-50	2	40
β-strand	55	1	38
α-helix	60	1
β-strand	61-62	2	40
α-helix	63	1
β-strand	64	1	41
β-strand	70-74	5	42
β-strand	77	1	43
β-strand	80	1	43
β-strand	83-86	4	42
α-helix	87	1
β-strand	91-93	3	44
β-strand	96-101	6	44
β-strand	118	1	45
β-strand	121	1	45

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
Death receptor 5	A, B, C, G, H, I	protein	130	Homo sapiens	O14763 (AlphaFold model)
Tnf-related apoptosis inducing ligand	D, E, F, J, K, L	protein	168	Homo sapiens	P50591 (AlphaFold model)

Sequence of entity 1 (A, B, C, G, H, I), FASTA

>1DU3_1 DEATH RECEPTOR 5 (chains A, B, C, G, H, I)
ALITQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFC
LRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPW
SDIECVHKES

Sequence of entity 2 (D, E, F, J, K, L), FASTA

>1DU3_2 TNF-RELATED APOPTOSIS INDUCING LIGAND (chains D, E, F, J, K, L)
VRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGE
LVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSK
DAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Crystal structure of TRAIL-DR5 complex identifies a critical role of the unique frame insertion in conferring recognition specificity. Cha, S.-S., Sung, B.-J., Kim, Y.A. et al. J Biol Chem (2000) 275:31171-31177. DOI 10.1074/jbc.M004414200 · 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
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
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

About this viewer

MolViewer shows 1DU3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.