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1du3

Crystal structure of TRAIL-SDR5

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1du3
deposition_date	2000-01-14
title	Crystal structure of TRAIL-SDR5
keywords	TRAIL, DR5, complex, APOPTOSIS; APOPTOSIS
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	42.19 Å
rg_electron	41.82 Å
i0	481904000.00
molecular_weight	170440.0 kDa
excluded_volume	208730 Å³
envelope_volume	277660 Å³
shell_volume	55382 Å³
envelope_diameter	147.8 Å
shell_rg	46.70 Å
envelope_rg	41.44 Å
shape_rg	41.79 Å
total_rg	42.16 Å
total_atoms	11946
n_residues	1490
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	141.8 Å
rg_real	42.35 Å
rg_real_error	1.71 Å
i0_real	4.8190e+08
i0_real_error	9.6920e+06
rg_reciprocal	42.19 Å
i0_reciprocal	481800000.0000
total_estimate	0.8658
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.3 Å
skewness	0.398
kurtosis	-0.547
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	61610000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.870

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DEATH RECEPTOR 5
formula_weight	14578.3 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,G,H,I
atom_count	12108

ALITQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKES

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	TNF-RELATED APOPTOSIS INDUCING LIGAND
formula_weight	19520.9 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	D,E,F,J,K,L

VRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Bacteria

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	162

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6. Citations (1)

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length_a	68.630 Å
length_b	124.810 Å
length_c	128.370 Å
angle_alpha	90.00 °
angle_beta	104.49 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.200 Å
resolution_low	8.000 Å
r_factor	0.2120
r_work	0.2910
r_free	0.2910

fit	/app/data/saxs_computation/du/1du3/1du3.fit
pddf	/app/data/pr_computation/du/1du3/1du3.pr.out
profile	/app/data/saxs_computation/du/1du3/1du3.dat

Crystal structure of TRAIL-SDR5

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)