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1d2q

CRYSTAL STRUCTURE OF HUMAN TRAIL

Method: X-RAY DIFFRACTION Dmax: 88.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TNF-RELATED APOPTOSIS INDUCING LIGAND

Homo sapiens

UniProt P50591

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 114–281 Fragment：EXTRA CELLULAR DOMAIN No other associated polymer 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
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 114–281 Fragment：EXTRA CELLULAR DOMAIN No other associated polymer 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
3 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 114–281 Fragment：EXTRA CELLULAR DOMAIN No other associated polymer 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

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 1D2Q 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
1D4V Crystal structure of trail-DR5 complex Deposited 1999-10-06 Different construct Different oligomeric state 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
1DG6 CRYSTAL STRUCTURE OF APO2L/TRAIL Deposited 1999-11-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 91–281（191 aa） 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
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 oligomeric state 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 oligomeric state 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 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 9 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 1–168； UniProt 114–281 Author chain B； PDBConstruct 1–168； UniProt 114–281

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1d2q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d2q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d2q
Deposition date deposition_date1999-09-27
Structure title titleCRYSTAL STRUCTURE OF HUMAN TRAIL
Keywords keywordsTRAIL, CYTOKINE; CYTOKINE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.07 Å
Radius of gyration Rg (electron density) rg_electron26.18 Å
Forward intensity I(0) i016075200.00
Molecular weight molecular_weight30605.0 kDa
Excluded volume excluded_volume38298 ų
Envelope volume envelope_volume49311 ų
Hydration-shell volume shell_volume17356 ų
Envelope diameter envelope_diameter89.7 Å
Shell Rg shell_rg30.50 Å
Envelope Rg envelope_rg26.01 Å
Shape Rg shape_rg26.19 Å
Total Rg total_rg26.70 Å
Total atoms total_atoms2674
Residues n_residues268
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.6 Å
Rg (real space) rg_real26.38 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real1.6080e+07
I(0) uncertainty (real space) i0_real_error2.5040e+05
Rg (reciprocal space) rg_reciprocal26.29 Å
I(0) (reciprocal space) i0_reciprocal16070000.0000
Solution quality estimate total_estimate0.7899
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.518
Kurtosis Kurtosis kurtosis-0.521
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3402000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.630; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.460; Smooth: 0.926
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d2qa_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like
Domain ID domain_idd1d2qb_
Class classb — All beta proteins
Fold Fold foldb.22 — TNF-like
Superfamily Superfamily superfamilyb.22.1 — TNF-like
Family Family familyb.22.1.1 — TNF-like

CATH v4.4 (2 domains)

Domain ID domain_id1d2qA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
Domain ID domain_id1d2qB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)