SAXSdb — 5cir

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

Tumor necrosis factor ligand superfamily member 10

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tumor necrosis factor receptor superfamily member 10A × 3 （O00220） ZINC ION × 1 CHLORIDE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNF10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–169； UniProt 114–281 Author chain B； PDBConstruct 2–169； UniProt 114–281 Author chain D； PDBConstruct 2–169； UniProt 114–281

Tumor necrosis factor receptor superfamily member 10A

Homo sapiens

UniProt O00220

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tumor necrosis factor ligand superfamily member 10 × 3 （P50591） ZINC ION × 1 CHLORIDE ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TR10A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–108； UniProt 125–232 Author chain F； PDBConstruct 1–108； UniProt 125–232 Author chain G； PDBConstruct 1–108； UniProt 125–232

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	5cir
Deposition date deposition_date	2015-07-13
Structure title title	Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)
Keywords keywords	Apoptosis, binding and specificity, ligand-receptor complex, TNF receptor family; APOPTOSIS
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.

5cir__assembly_1__model_1

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

Download this curve (.dat)

5cir__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cir__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.40 Å
Rg (electron density)	25.88 Å
Total Rg	26.95 Å
Atom count	5603
Residues	752
Excluded volume	98179 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cir__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor ligand superfamily member 10
Molecular weight formula_weight	19652.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D
Atom count atom_count	5611

MVRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 10A
Molecular weight formula_weight	11749.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G

HSPLGELCPPGSHRSERPGACNRCTEGVGYTNASNNLFACLPCTACKSDEEERSPCTTTRNTACQCKPGTFRNDNSAEMCRKCSTGCPRGMVKVKDCTPWSDIECVHK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5cira_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d5cirb_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d5cird_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

CATH v4.4 (9 domains)

Domain ID domain_id	5cirA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5cirB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5cirD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5cirE01
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	5cirE02
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	5cirF01
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	5cirF02
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	5cirG01
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	5cirG02
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	84.600 Å
Unit-cell length b length_b	87.600 Å
Unit-cell length c length_c	107.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	27.600 Å
R factor r_factor	0.1792
R_work r_work	0.1767
R_free r_free	0.2163

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)

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

Tumor necrosis factor ligand superfamily member 10

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 10A

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

5cir__assembly_1__model_1

5cir__assembly_1__model_1 | I(q)

5cir__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)

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

Tumor necrosis factor ligand superfamily member 10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tumor necrosis factor receptor superfamily member 10A

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

5cir__assembly_1__model_1

5cir__assembly_1__model_1 | I(q)

5cir__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)