1ZA3: YSd1 Fab

The crystal structure of the YSd1 Fab bound to DR5. Determined by X-ray diffraction at 3.35 Å resolution. Released 14 Jun 2005.

Method: X-ray diffraction
Resolution: 3.35 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,149
Mol. weight: 126.74 kDa
Released: 14 Jun 2005

Explore 1ZA3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ZA3 contains 36 α-helices and 118 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: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	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
β-strand	62-63	2	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	97	1	2
β-strand	101-106	6	2
β-strand	110	1	3
α-helix	111-112	2
β-strand	113-117	5	4
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	4
β-strand	139	1	3
β-strand	144-149	6	5
β-strand	153	1	5
β-strand	158-162	5	4
α-helix	163-166	4
β-strand	172-181	10	4
α-helix	182-185	4
β-strand	190-196	7	5
β-strand	204-209	6	5

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
β-strand	33-39	7	7
β-strand	45-52	8	7
β-strand	56-59	4	7
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
α-helix	99-100D	6
β-strand	100L-103	4	7
β-strand	107-111	5	7
α-helix	115-116	2
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	186-188	3
β-strand	195-200	6	10
α-helix	201-203	3
β-strand	205-210	6	10

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	11-12	2	26
β-strand	18-25	8	25
α-helix	29-31	3
β-strand	33-39	7	27
β-strand	46-52	7	27
β-strand	56-59	4	27
β-strand	67-72	6	25
β-strand	77-82	6	25
β-strand	88-95	8	27
α-helix	99-100D	6
β-strand	100L-103	4	27
β-strand	107-109	3	27
β-strand	110-111	2	26
β-strand	117	1	28
α-helix	118-119	2
β-strand	120-124	5	29
β-strand	136-145	10	29
β-strand	146	1	28
β-strand	150-154	5	30
α-helix	155-157	3
β-strand	159	1	30
β-strand	163-165	3	29
α-helix	166-168	3
β-strand	176-184	9	29
α-helix	186-188	3
β-strand	195-200	6	30
β-strand	205-210	6	30

Chain L: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	33-38	6	19
α-helix	43-44	2
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-64	3	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	85-90	6	19
α-helix	96	1
β-strand	97	1	19
α-helix	98	1
β-strand	101-105	5	19
β-strand	110	1	20
β-strand	113-117	5	21
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	21
β-strand	139	1	20
β-strand	144	1	22
β-strand	147	1	23
β-strand	148-149	2	24
β-strand	152-153	2	24
β-strand	158-162	5	21
α-helix	163-166	4
β-strand	172-181	10	21
α-helix	182-186	5
β-strand	190-194	5	23
β-strand	196	1	22
β-strand	205-209	5	23

Chain R: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	11
β-strand	27	1	11
β-strand	28	1	12
β-strand	32-34	3	13
β-strand	41-43	3	13
β-strand	49-50	2	14
β-strand	55	1	12
α-helix	60	1
β-strand	61-62	2	14
α-helix	63-67	5
β-strand	71-74	4	15
β-strand	83-85	3	15
α-helix	86-87	2
β-strand	90-93	4	16
β-strand	96-102	7	16
β-strand	118	1	17
β-strand	121	1	17

Chain S: 4 helices, 16 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
β-strand	49-50	2	34
β-strand	55	1	32
α-helix	60	1
β-strand	61-62	2	34
α-helix	63-67	5
β-strand	70-74	5	35
β-strand	83-86	4	35
α-helix	87	1
β-strand	90-93	4	36
β-strand	96-102	7	36
α-helix	103-104	2
β-strand	113-115	3	37
β-strand	118	1	38
β-strand	121	1	38
β-strand	124-125	2	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab-YSd1 light chain	A, L	protein	213	Homo sapiens
Fab-YSd1 heavy chain	B, H	protein	236	Homo sapiens
Tumor necrosis factor receptor superfamily member 10B	R, S	protein	134	Homo sapiens	O14763 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>1ZA3_1 Fab-YSd1 light chain (chains A, L)
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYAASYLYSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQSSSSPYTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, H), FASTA

>1ZA3_2 Fab-YSd1 heavy chain (chains B, H)
EVQLVESGGGLVQPGGSLRLSCAASGFSIYSYSIHWVRQAPGKGLEWVASISPYSGYTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRYSSYYSYYYSSSSYSYAMDYWG
QGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (R, S), FASTA

>1ZA3_3 Tumor necrosis factor receptor superfamily member 10B (chains R, S)
GSHMALITQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWND
LLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGD
CTPWSDIECVHKES

Primary citation

Molecular recognition by a binary code. Fellouse, F.A., Li, B., Compaan, D.M. et al. J Mol Biol (2005) 348:1153-1162. DOI 10.1016/j.jmb.2005.03.041 · 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…
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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