SAXSdb — 2hev

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

Tumor necrosis factor ligand superfamily member 4

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain F； UniProt 51–183	Fragment：extracellular domain (residues 51-183) Mutation：N90D, N114D	Tumor necrosis factor receptor superfamily member 4 × 3 （P43489） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.251

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	TNFL4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 5–137； UniProt 51–183

Tumor necrosis factor receptor superfamily member 4

Homo sapiens

UniProt P43489

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain R； UniProt 29–170	Fragment：extracellular domain (residues 29-170)	Tumor necrosis factor ligand superfamily member 4 × 3 （P23510） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.251

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2HEV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain H 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain I 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain K 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain L 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain H 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain I 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain J 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain K 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain L 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain H 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain I 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain J 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain K 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE Chain L 262–266（5 aa） Fragment：TRAF-BINDING SEQUENCE	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
2HEY Crystal structure of murine OX40L bound to human OX40 Deposited 2006-06-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 29–170（142 aa） Fragment：extracellular domain (residues 29-170)	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M NaCl, 1.4 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.247
2HEY Crystal structure of murine OX40L bound to human OX40 Deposited 2006-06-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain T 29–170（142 aa） Fragment：extracellular domain (residues 29-170)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M NaCl, 1.4 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.247
6OGX Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2 Deposited 2019-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 29–170（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Tris pH 8.5, 1.5 M D-L malic acid pH 7.0, 0.15 mM dimethylethylammonium propane sulfate (NDSB-195)	Resolution 2.77 Å R-free 0.254
6OKM Human OX40R (TNFRSF4) bound to Fab 3C8 Deposited 2019-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 29–170（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K	Resolution 2.10 Å R-free 0.238
6OKN OX40R (TNFRSF4) bound to Fab 1A7 Deposited 2019-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 29–170（142 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；tbd	Resolution 3.25 Å R-free 0.228
6OKN OX40R (TNFRSF4) bound to Fab 1A7 Deposited 2019-04-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 29–170（142 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；tbd	Resolution 3.25 Å R-free 0.228
7YK4 ox40-antibody Deposited 2022-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–170（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M potassium sodium tartrate, 14% PEG 3350, 10% glycerol	Resolution 2.70 Å R-free 0.298
7YK4 ox40-antibody Deposited 2022-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 29–170（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M potassium sodium tartrate, 14% PEG 3350, 10% glycerol	Resolution 2.70 Å R-free 0.298
8AG1 Crystal structure of a novel OX40 antibody Deposited 2022-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–170（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350	Resolution 3.30 Å R-free 0.268
8AG1 Crystal structure of a novel OX40 antibody Deposited 2022-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain a 29–170（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350	Resolution 3.30 Å R-free 0.268

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain R； PDBConstruct 5–146； UniProt 29–170

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	2hev
Deposition date deposition_date	2006-06-22
Structure title title	Crystal structure of the complex between OX40L and OX40
Keywords keywords	cytokine, receptor-ligand complex, TNFSF, TNFRSF; CYTOKINE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.52 Å
Radius of gyration Rg (electron density) rg_electron	23.71 Å
Forward intensity I(0) i0	17561600.00
Molecular weight molecular_weight	30052.0 kDa
Excluded volume excluded_volume	36904 Å³
Envelope volume envelope_volume	50370 Å³
Hydration-shell volume shell_volume	18950 Å³
Envelope diameter envelope_diameter	90.8 Å
Shell Rg shell_rg	28.76 Å
Envelope Rg envelope_rg	24.12 Å
Shape Rg shape_rg	23.70 Å
Total Rg total_rg	24.41 Å
Total atoms total_atoms	2095
Residues n_residues	266
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	87.1 Å
Rg (real space) rg_real	24.67 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.7560e+07
I(0) uncertainty (real space) i0_real_error	2.6000e+05
Rg (reciprocal space) rg_reciprocal	24.64 Å
I(0) (reciprocal space) i0_reciprocal	17560000.0000
Solution quality estimate total_estimate	0.8534
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.445
Kurtosis Kurtosis kurtosis	-0.142
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1339000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.726; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor ligand superfamily member 4
Molecular weight formula_weight	15858.0 kDa
Mutation mutation	N90D, N114D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	2182

GSHMQVSHRYPRIQSIKVQFTEYKKEKGFILTSQKEDEIMKVQDNSVIINCDGFYLISLKGYFSQEVDISLHYQKDEEPLFQLKKVRSVNSLMVASLTYKDKVYLNVTTDNTSLDDFHVNGGELILIHQNPGEFCVL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 4
Molecular weight formula_weight	15808.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

GSHMLHCVGDTYPSNDRCCHECRPGNGMVSRCSRSQNTVCRPCGPGFYNDVVSSKPCKPCTWCNLRSGSERKQLCTATQDTVCRCRAGTQPLDSYKPGVDCAPCPPGHFSPGDNQACKPWTNCTLAGKHTLQPASNSSDAICEDRD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

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	man
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hevf1
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	d2hevr1
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	d2hevr2
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	d2hevr3
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 (3 domains)

Domain ID domain_id	2hevF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	2hevR01
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	2hevR02
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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8. Citations (1)

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Unit-cell length a length_a	111.903 Å
Unit-cell length b length_b	111.903 Å
Unit-cell length c length_c	233.238 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.410 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2125
R_work r_work	0.2082
R_free r_free	0.2511

fit	/app/data/saxs_computation/he/2hev/2hev.fit
pddf	/app/data/pr_computation/he/2hev/2hev.pr.out
profile	/app/data/saxs_computation/he/2hev/2hev.dat

Crystal structure of the complex between OX40L and OX40

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

Tumor necrosis factor ligand superfamily member 4

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)