SAXSdb — 1dg6

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

APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 91–281	Fragment：TRIMERIC JELLY-ROLL DOMAIN OF APO2L Mutation：D218A	ZN ZINC ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；WELL SOLUTION 32% MPD; DROP 1.2MG/ML APO2L, 20MM TRIS HCL PH 7.5, 1% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.30 Å R-free 0.197

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 1DG6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0G CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 (DR5) BOUND TO APO2L/TRAIL Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 114–281（168 aa） Fragment：RESIDUES 114-281 Chain B 114–281（168 aa） Fragment：RESIDUES 114-281 Chain D 114–281（168 aa） Fragment：RESIDUES 114-281	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；15% Peg8K, 10% ethylene glycol, 0.2M ammonium sulface, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.40 Å R-free 0.267
1D2Q CRYSTAL STRUCTURE OF HUMAN TRAIL Deposited 1999-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 114–281（168 aa） Fragment：EXTRA CELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；295 K；PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K	Resolution 2.80 Å R-free 0.282
1D2Q CRYSTAL STRUCTURE OF HUMAN TRAIL Deposited 1999-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 114–281（168 aa） Fragment：EXTRA CELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；295 K；PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K	Resolution 2.80 Å R-free 0.282
1D2Q CRYSTAL STRUCTURE OF HUMAN TRAIL Deposited 1999-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 114–281（168 aa） Fragment：EXTRA CELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；295 K；PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K	Resolution 2.80 Å R-free 0.282
1D4V Crystal structure of trail-DR5 complex Deposited 1999-10-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 119–281（163 aa） Fragment：SINGLE SUBUNIT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% ETHYLENE GLYCOL, 0.1% N-OCTYL-BETA-GLUCOSIDE, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 20K	Resolution 2.20 Å R-free 0.270
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 114–281（168 aa） Chain E 114–281（168 aa） Chain F 114–281（168 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；295 K；PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K	Resolution 2.20 Å R-free 0.291
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 114–281（168 aa） Chain K 114–281（168 aa） Chain L 114–281（168 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；295 K；PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K	Resolution 2.20 Å R-free 0.291
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 114–281（168 aa） Fragment：UNP residues 114-281	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 114–281（168 aa） Fragment：UNP residues 114-281	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 114–281（168 aa） Fragment：UNP residues 114-281	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
5CIR Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10) Deposited 2015-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 114–281（168 aa） Fragment：Residues 114-281 Chain B 114–281（168 aa） Fragment：Residues 114-281 Chain D 114–281（168 aa） Fragment：Residues 114-281	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；100 mM MMT (1:2:2 ratio of DL-malic acid, MES, Tris base), pH 5.0, 22.2%(W/V) PEG 2000MME	Resolution 3.00 Å R-free 0.216

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNF10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 91–281

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	1dg6
Deposition date deposition_date	1999-11-23
Structure title title	CRYSTAL STRUCTURE OF APO2L/TRAIL
Keywords keywords	CYTOKINE, TNF, TRIMER, ZINC-BINDING SITE, APOPTOSIS; APOPTOSIS
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	18.15 Å
Radius of gyration Rg (electron density) rg_electron	17.00 Å
Forward intensity I(0) i0	5924500.00
Molecular weight molecular_weight	17515.0 kDa
Excluded volume excluded_volume	21839 Å³
Envelope volume envelope_volume	25932 Å³
Hydration-shell volume shell_volume	13563 Å³
Envelope diameter envelope_diameter	68.2 Å
Shell Rg shell_rg	22.33 Å
Envelope Rg envelope_rg	17.83 Å
Shape Rg shape_rg	16.92 Å
Total Rg total_rg	18.16 Å
Total atoms total_atoms	1234
Residues n_residues	149
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	69.1 Å
Rg (real space) rg_real	18.26 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	5.9250e+06
I(0) uncertainty (real space) i0_real_error	8.1810e+04
Rg (reciprocal space) rg_reciprocal	18.25 Å
I(0) (reciprocal space) i0_reciprocal	5924000.0000
Solution quality estimate total_estimate	0.8019
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.536
Kurtosis Kurtosis kurtosis	0.014
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1802000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.554; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.760; Smooth: 0.999

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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	APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)
Molecular weight formula_weight	22106.8 kDa
Mutation mutation	D218A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1477

MILRTSEETISTVQEKQQNISPLVRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPAPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

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	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dg6a_
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 (1 domains)

Domain ID domain_id	1dg6A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	66.435 Å
Unit-cell length b length_b	66.435 Å
Unit-cell length c length_c	197.727 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	1.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1410
R_work r_work	0.1410
R_free r_free	0.1970

fit	/app/data/saxs_computation/dg/1dg6/1dg6.fit
pddf	/app/data/pr_computation/dg/1dg6/1dg6.pr.out
profile	/app/data/saxs_computation/dg/1dg6/1dg6.dat

CRYSTAL STRUCTURE OF APO2L/TRAIL

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

APO2L/TNF-RELATED APOPOTIS INDUCING LIGAND (TRAIL)

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