8DPX: Preligand association structure of DR5

Preligand association structure of DR5. Determined by solution NMR. Released 15 Feb 2023.

Method: Solution NMR
Organism: Homo sapiens
Chains: 3
Atoms: 2,520
Mol. weight: 36.7 kDa
Released: 15 Feb 2023

Explore 8DPX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DPX contains 8 α-helices and 38 β-strands across 3 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	81	1	1
β-strand	85-87	3	2
β-strand	94-96	3	2
β-strand	103	1	3
β-strand	108	1	1
β-strand	114	1	3
α-helix	115-117	3
β-strand	123-125	3	4
β-strand	130	1	5
β-strand	133	1	5
β-strand	137-139	3	4
β-strand	143-144	2	6
β-strand	154-155	2	6
α-helix	156-157	2
β-strand	164-166	3	7
β-strand	178-180	3	7

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	81	1	8
β-strand	85-87	3	9
β-strand	94-96	3	9
β-strand	102-103	2	10
β-strand	108	1	8
β-strand	114-115	2	10
α-helix	116-117	2
β-strand	123-127	5	11
β-strand	136-139	4	11
β-strand	143-144	2	12
β-strand	154-155	2	12
α-helix	156-157	2
α-helix	160	1
β-strand	164-166	3	13
β-strand	178-180	3	13

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	81	1	14
β-strand	85-87	3	15
β-strand	94-96	3	15
β-strand	103	1	16
β-strand	108	1	14
β-strand	114	1	16
α-helix	115-117	3
β-strand	123-127	5	17
β-strand	136-139	4	17
β-strand	143-144	2	18
β-strand	154-155	2	18
α-helix	156-157	2
α-helix	160	1
β-strand	165-168	4	19
β-strand	177-179	3	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 10B	A, B, C	protein	109	Homo sapiens	O14763 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8DPX_1 Tumor necrosis factor receptor superfamily member 10B (chains A, B, C)
SEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTV
CQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKESGD

Primary citation

Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation. Du, G., Zhao, L., Zheng, Y. et al. Cell Res (2023) 33:131-146. DOI 10.1038/s41422-022-00755-2 · 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
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

Browse structure collections

About this viewer

MolViewer shows 8DPX 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.