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1d4v

Crystal structure of trail-DR5 complex

Method: X-RAY DIFFRACTION D_max: 83.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d4v
deposition_date	1999-10-06
title	Crystal structure of trail-DR5 complex
keywords	LIGAND-RECEPTOR COMPLEX, TRIMERIC JELLY-ROLL, TNF-R SUPERFAMILY, 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	24.10 Å
rg_electron	23.60 Å
i0	20106200.00
molecular_weight	32017.0 kDa
excluded_volume	39146 Å³
envelope_volume	51033 Å³
shell_volume	19245 Å³
envelope_diameter	86.6 Å
shell_rg	28.73 Å
envelope_rg	24.23 Å
shape_rg	23.56 Å
total_rg	24.36 Å
total_atoms	2242
n_residues	280
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	83.8 Å
rg_real	24.21 Å
rg_real_error	0.70 Å
i0_real	2.0110e+07
i0_real_error	2.9920e+05
rg_reciprocal	24.19 Å
i0_reciprocal	20110000.0000
total_estimate	0.8746
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.416
kurtosis	-0.275
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	1708000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.836; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	TNF-RELATED APOPTOSIS INDUCING LIGAND
formula_weight	18921.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	2396

PQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	DEATH RECEPTOR 5
formula_weight	13143.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

PQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKESGD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	154

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6. Citations (1)

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length_a	95.520 Å
length_b	95.520 Å
length_c	69.810 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 3 2 1
int_tables_number	150
crystal_system	—

resolution	2.200 Å
resolution_low	15.000 Å
r_factor	0.2210
r_work	0.2210
r_free	0.2700

fit	/app/data/saxs_computation/d4/1d4v/1d4v.fit
pddf	/app/data/pr_computation/d4/1d4v/1d4v.pr.out
profile	/app/data/saxs_computation/d4/1d4v/1d4v.dat

Crystal structure of trail-DR5 complex

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)