1za3

The crystal structure of the YSd1 Fab bound to DR5

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tumor necrosis factor receptor superfamily member 10B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Fab-YSd1 light chain × 1 Fab-YSd1 heavy chain × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Fab-YSd1 light chain × 1 Fab-YSd1 heavy chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TR10B_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain R； PDBConstruct 5–134； UniProt 54–183 Author chain S； PDBConstruct 5–134； UniProt 54–183

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1za3
Deposition date deposition_date	2005-04-05
Structure title title	The crystal structure of the YSd1 Fab bound to DR5
Keywords keywords	;phage display, protein engineering, combinatorial mutagenesis, antibody library, death receptor-5, IMMUNE SYSTEM-SIGNALING PROTEIN COMPLEX ;; IMMUNE SYSTEM/SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1za3__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1za3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1za3__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.85 Å
Rg (electron density)	28.00 Å
Total Rg	28.86 Å
Atom count	4128
Residues	543
Excluded volume	72637 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1za3__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1za3__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Fab-YSd1 light chain
Molecular weight formula_weight	23148.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	8149

DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYAASYLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQSSSSPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 2 Entity 2 polymer

Description description	Fab-YSd1 heavy chain
Molecular weight formula_weight	25231.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,H

EVQLVESGGGLVQPGGSLRLSCAASGFSIYSYSIHWVRQAPGKGLEWVASISPYSGYTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRYSSYYSYYYSSSSYSYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 3 Entity 3 polymer

Description description	Tumor necrosis factor receptor superfamily member 10B
Molecular weight formula_weight	14991.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S

GSHMALITQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKES

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

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6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d1za3a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1za3a2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1za3b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1za3b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1za3h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1za3h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1za3l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1za3l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1za3r1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d1za3r2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d1za3r3
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d1za3s1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d1za3s2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

Domain ID domain_id	d1za3s3
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.1 — TNF receptor-like

CATH v4.4 (12 domains)

Domain ID domain_id	1za3A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1za3R01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	1za3R02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	1za3S01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	1za3S02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

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Unit-cell length a length_a	147.059 Å
Unit-cell length b length_b	147.059 Å
Unit-cell length c length_c	144.947 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.350 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2298
R_work r_work	0.2241
R_free r_free	0.2803

The crystal structure of the YSd1 Fab bound to DR5

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tumor necrosis factor receptor superfamily member 10B

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1za3__assembly_1__model_1

1za3__assembly_1__model_1 | I(q)

1za3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)

The crystal structure of the YSd1 Fab bound to DR5

1. Protein Identity and Related Structures Protein Identity & Related Structures

Tumor necrosis factor receptor superfamily member 10B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1za3__assembly_1__model_1

1za3__assembly_1__model_1 | I(q)

1za3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)