SAXSdb — 7khd

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

Tumor necrosis factor ligand superfamily member 18

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 18 × 3 （Q9Y5U5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Tumor necrosis factor receptor superfamily member 18 × 3 （Q9Y5U5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNF18_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 72–199 Author chain B； PDBConstruct 1–128； UniProt 72–199

Tumor necrosis factor receptor superfamily member 18

Homo sapiens

UniProt Q9Y5U5

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 18 × 3 （Q9UNG2） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Tumor necrosis factor ligand superfamily member 18 × 3 （Q9UNG2） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TNR18_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–137； UniProt 26–162 Author chain D； PDBConstruct 1–137； UniProt 26–162

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	7khd
Deposition date deposition_date	2020-10-21
Structure title title	Human GITR-GITRL complex
Keywords keywords	TNFRSF, receptor-ligand complex, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

7khd__assembly_1__model_1

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

Download this curve (.dat)

7khd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7khd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.30 Å
Rg (electron density)	33.93 Å
Total Rg	34.26 Å
Atom count	5187
Residues	660
Excluded volume	91829 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7khd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7khd__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor ligand superfamily member 18
Molecular weight formula_weight	14515.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3442

QLETAKEPCMAKFGPLPSKWQMASSEPPCVNKVSDWKLEILQNGLYLIYGQVAPNANYNDVAPFEVRLYKNKDMIQTLTNKSKIQNVGGTYELHVGDTIDLIFNSEHQVLKNNTYWGIILLANPQFIS

Source Source

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

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 18
Molecular weight formula_weight	14645.5 kDa
Mutation mutation	C57S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QRPTGGPGCGPGRLLLGTGTDARCCRVHTTRCCRDYPGEECCSEWDCMCVQPEFHCGDPCCTTCRHHPCPPGQGVQSQGKFSFGFQCIDCASGTFSGGHEGHCKPWTDCTQFGFLTVFPGNKTHNAVCVPGSPPAEP

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d7khda_
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	d7khdb_
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

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Unit-cell length a length_a	168.420 Å
Unit-cell length b length_b	168.420 Å
Unit-cell length c length_c	168.420 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	48

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	cubic

Resolution resolution	2.956 Å
Low-resolution limit resolution_low	37.660 Å
R factor r_factor	0.2195
R_work r_work	0.2177
R_free r_free	0.2541

Human GITR-GITRL complex

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

Tumor necrosis factor ligand superfamily member 18

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 18

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

7khd__assembly_1__model_1

7khd__assembly_1__model_1 | I(q)

7khd__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 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Human GITR-GITRL complex

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

Tumor necrosis factor ligand superfamily member 18

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 18

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

7khd__assembly_1__model_1

7khd__assembly_1__model_1 | I(q)

7khd__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 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)