2H9G: Fab BdF1, light chain

Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5). Determined by X-ray diffraction at 2.32 Å resolution. Released 8 Aug 2006.

Method: X-ray diffraction
Resolution: 2.32 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,899
Mol. weight: 124.01 kDa
Released: 8 Aug 2006

Explore 2H9G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2H9G contains 46 α-helices and 116 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.

Chains A and L: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
α-helix	107	1
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-186	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-52	8	7
β-strand	56-59	4	7
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
β-strand	97	1	8
β-strand	100C-101	2	7
β-strand	107-111	5	7
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chain H: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	24
β-strand	11-12	2	25
β-strand	18-25	8	24
β-strand	34-39	6	26
β-strand	45-52	8	26
β-strand	56-59	4	26
β-strand	64	1	24
β-strand	67-72	6	24
β-strand	77-82	6	24
α-helix	84-86	3
β-strand	88-95	8	26
β-strand	97	1	27
β-strand	100C-101	2	26
β-strand	107-109	3	26
β-strand	110-111	2	25
α-helix	115-116	2
β-strand	117	1	28
α-helix	118-119	2
β-strand	120-124	5	29
β-strand	135-145	11	29
β-strand	146	1	28
β-strand	151-154	4	30
α-helix	155-157	3
β-strand	159	1	30
β-strand	163-165	3	29
α-helix	166-168	3
β-strand	169-170	2	29
β-strand	176-185	10	29
α-helix	186-188	3
β-strand	195-200	6	30
α-helix	201-203	3
β-strand	205-210	6	30

Chain R: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	12
β-strand	27	1	12
β-strand	28	1	13
α-helix	29	1
β-strand	32-34	3	14
β-strand	41-43	3	14
β-strand	49-50	2	15
β-strand	55	1	13
β-strand	57	1	8
α-helix	60	1
β-strand	61-62	2	15
α-helix	63-65	3
β-strand	70-74	5	16
β-strand	83-86	4	16
α-helix	87	1
β-strand	90-91	2	17
α-helix	99-100	2
β-strand	101-102	2	17
α-helix	103-104	2
β-strand	112-113	2	18
α-helix	122-124	3
β-strand	125-126	2	18

Chain S: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	31
β-strand	27	1	31
β-strand	28	1	32
β-strand	32-34	3	33
β-strand	41-43	3	33
α-helix	44-45	2
β-strand	49-50	2	34
β-strand	55	1	32
β-strand	57	1	27
α-helix	60	1
β-strand	61-62	2	34
α-helix	63	1
β-strand	74	1	35
β-strand	83	1	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab BdF1, light chain	A, L	protein	214	Homo sapiens
Fab BdF1, heavy chain	B, H	protein	228	Homo sapiens
Tumor necrosis factor receptor superfamily member 10B precursor	R, S	protein	130	Homo sapiens	O14763 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>2H9G_1 Fab BdF1, light chain (chains A, L)
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, H), FASTA

>2H9G_2 Fab BdF1, heavy chain (chains B, H)
EVQLVESGGGLVQPGGSLRLSCAASGFSIGKSGIHWVRQAPGKGLEWVAVIYPHDGNTAY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRLALVRMWMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHL

Sequence of entity 3 (R, S), FASTA

>2H9G_3 Tumor necrosis factor receptor superfamily member 10B precursor (chains R, S)
ALITQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFC
LRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPW
SDIECVHKES

Primary citation

Activation of the Proapoptotic Death Receptor DR5 by Oligomeric Peptide and Antibody Agonists. Li, B., Russell, S.J., Compaan, D.M. et al. J Mol Biol (2006) 361:522-536. DOI 10.1016/j.jmb.2006.06.042 · 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
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

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