1du3

Crystal structure of TRAIL-SDR5

Method: X-RAY DIFFRACTION Dmax: 141.8 Å Quality: GOOD

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

DEATH RECEPTOR 5

Homo sapiens

UniProt O14763

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 A; UniProt 54–183 Chain B; UniProt 54–183 Chain C; UniProt 54–183 Fragment:EXTRACELLULAR DOMAIN TNF-RELATED APOPTOSIS INDUCING LIGAND × 3 (P50591) 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
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 54–183 Chain H; UniProt 54–183 Chain I; UniProt 54–183 Fragment:EXTRACELLULAR DOMAIN TNF-RELATED APOPTOSIS INDUCING LIGAND × 3 (P50591) 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

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.

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TR10B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–130; UniProt 54–183 Author chain B; PDBConstruct 1–130; UniProt 54–183 Author chain C; PDBConstruct 1–130; UniProt 54–183 Author chain G; PDBConstruct 1–130; UniProt 54–183 Author chain H; PDBConstruct 1–130; UniProt 54–183 Author chain I; PDBConstruct 1–130; UniProt 54–183

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain D; UniProt 114–281 Chain E; UniProt 114–281 Chain F; UniProt 114–281 Not recorded DEATH RECEPTOR 5 × 3 (O14763) 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
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain J; UniProt 114–281 Chain K; UniProt 114–281 Chain L; UniProt 114–281 Not recorded DEATH RECEPTOR 5 × 3 (O14763) 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

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.

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TNF10_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–168; UniProt 114–281 Author chain E; PDBConstruct 1–168; UniProt 114–281 Author chain F; PDBConstruct 1–168; UniProt 114–281 Author chain J; PDBConstruct 1–168; UniProt 114–281 Author chain K; PDBConstruct 1–168; UniProt 114–281 Author chain L; 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 1du3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1du3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1du3
Deposition date deposition_date2000-01-14
Structure title titleCrystal structure of TRAIL-SDR5
Keywords keywordsTRAIL, DR5, complex, APOPTOSIS; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.19
Radius of gyration Rg (electron density) rg_electron41.82
Forward intensity I(0) i0481904000.00
Molecular weight molecular_weight170440.0 kDa
Excluded volume excluded_volume208730 ų
Envelope volume envelope_volume277660 ų
Hydration-shell volume shell_volume55382 ų
Envelope diameter envelope_diameter147.8
Shell Rg shell_rg46.70
Envelope Rg envelope_rg41.44
Shape Rg shape_rg41.79
Total Rg total_rg42.16
Total atoms total_atoms11946
Residues n_residues1490
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax141.8
Rg (real space) rg_real42.35
Rg uncertainty (real space) rg_real_error1.71
I(0) (real space) i0_real4.8190e+08
I(0) uncertainty (real space) i0_real_error9.6920e+06
Rg (reciprocal space) rg_reciprocal42.19
I(0) (reciprocal space) i0_reciprocal481800000.0000
Solution quality estimate total_estimate0.8658
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.3
Skewness Skewness skewness0.398
Kurtosis Kurtosis kurtosis-0.547
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61610000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.818; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.870

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 44 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd1du3a1
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3a2
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3a3
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3b1
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3b2
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3b3
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3c1
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3c2
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3c3
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3d_
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_idd1du3e_
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_idd1du3f_
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_idd1du3g1
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3g2
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3g3
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3h1
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3h2
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3h3
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3i1
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3i2
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3i3
Class classg — Small proteins
Fold Fold foldg.24 — TNF receptor-like
Superfamily Superfamily superfamilyg.24.1 — TNF receptor-like
Family Family familyg.24.1.1 — TNF receptor-like
Domain ID domain_idd1du3j_
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_idd1du3k_
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_idd1du3l_
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 (20 domains)

Domain ID domain_id1du3A01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3A02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3B01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3B02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3B03
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3C01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3C02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40
Domain ID domain_id1du3E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40
Domain ID domain_id1du3F00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40
Domain ID domain_id1du3G01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3G02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3G03
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3H01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3H02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3I01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3I02
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Tumor Necrosis Factor Receptor, subunit A, domain 2
Domain ID domain_id1du3J00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40
Domain ID domain_id1du3K00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40
Domain ID domain_id1du3L00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)