4OD2: Fab fragment of an anti-DR5 antibody

Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5. Determined by X-ray diffraction at 3.2 Å resolution. Released 5 Feb 2014.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,896
Mol. weight: 59.36 kDa
Released: 5 Feb 2014

Explore 4OD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OD2 contains 15 α-helices and 59 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: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	8-12	5	2
β-strand	17-22	6	1
β-strand	29	1	3
β-strand	33-36	4	2
β-strand	43-46	4	2
β-strand	47	1	4
β-strand	51	1	4
β-strand	60-65	6	1
β-strand	68-73	6	1
α-helix	78-80	3
β-strand	82-86	5	2
β-strand	87-89	3	5
β-strand	96-98	3	5
β-strand	102-107	6	2
α-helix	110-111	2
β-strand	112	1	6
β-strand	115-119	5	7
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-140	10	7
β-strand	141	1	6
β-strand	145-151	7	8
β-strand	154-155	2	8
β-strand	160-162	3	7
β-strand	166-167	2	7
β-strand	173-181	9	7
α-helix	183-187	5
β-strand	192-198	7	8
β-strand	201-207	7	8

Chain B: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
β-strand	34-40	7	10
β-strand	43-51	9	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-83	6	9
β-strand	92-99	8	10
β-strand	108-111	4	10
β-strand	115-119	5	10
β-strand	125	1	11
β-strand	128-132	5	12
β-strand	144-153	10	12
β-strand	154	1	11
β-strand	159-162	4	13
α-helix	163-165	3
β-strand	171-173	3	12
α-helix	174-176	3
β-strand	177-178	2	12
β-strand	184-192	9	12
α-helix	194-197	4
β-strand	203-208	6	13
α-helix	209-211	3
β-strand	213-218	6	13

Chain S: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	14
β-strand	27	1	14
β-strand	28	1	15
α-helix	29	1
β-strand	32-34	3	16
β-strand	41-43	3	16
α-helix	44-45	2
β-strand	49-50	2	17
β-strand	55	1	15
α-helix	60	1
β-strand	61-62	2	17
α-helix	63-64	2
β-strand	66	1	3
β-strand	70-74	5	18
β-strand	83-86	4	18
β-strand	90-91	2	19
β-strand	101-102	2	19
α-helix	103-104	2
α-helix	107-108	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment of drozitumab, light chain	A	protein	213	Homo sapiens
Fab fragment of drozitumab, heavy chain	B	protein	232	Homo sapiens
Tumor necrosis factor receptor superfamily member 10B	S	protein	111	Homo sapiens	O14763 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4OD2_1 Fab fragment of drozitumab, light chain (chains A)
SELTQDPAVSVALGQTVRITCSGDSLRSYYASWYQQKPGQAPVLVIYGANNRPSGIPDRF
SGSSSGNTASLTITGAQAEDEADYYCNSADSSGNHVVFGGGTKLTVLGQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (B), FASTA

>4OD2_2 Fab fragment of drozitumab, heavy chain (chains B)
EVQLVQSGGGVERPGGSLRLSCAASGFTFDDYAMSWVRQAPGKGLEWVSGINWQGGSTGY
ADSVKGRVTISRDNAKNSLYLQMNSLRAEDTAVYYCAKILGAGRGWYFDYWGKGTTVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTAAP

Sequence of entity 3 (S), FASTA

>4OD2_3 Tumor necrosis factor receptor superfamily member 10B (chains S)
RSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTT
RNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKES

Primary citation

Structural and functional analysis of the interaction between the agonistic monoclonal antibody Apomab and the proapoptotic receptor DR5. Adams, C., Totpal, K., Lawrence, D. et al. Cell Death Differ (2008) 15:751-761. DOI 10.1038/sj.cdd.4402306 · 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
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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