SAXSdb — 9r18

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1. Structure Basics

entry_id	9r18
deposition_date	2025-04-25
title	Structure of Sortilin ECD in complex with TNFa-targeting SORTAC
keywords	Lysosome sorting receptor, Targeted protein degradation, SORtilin-based lysosome TArgeting Chimeras (SORTACs), PROTEIN BINDING; PROTEIN BINDING
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	28.83 Å
rg_electron	27.73 Å
i0	94156600.00
molecular_weight	75627.0 kDa
excluded_volume	94315 Å³
envelope_volume	124160 Å³
shell_volume	36477 Å³
envelope_diameter	101.4 Å
shell_rg	35.93 Å
envelope_rg	27.54 Å
shape_rg	27.73 Å
total_rg	28.56 Å
total_atoms	10447
n_residues	658
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	94.5 Å
rg_real	28.68 Å
rg_real_error	0.57 Å
i0_real	9.4160e+07
i0_real_error	1.2510e+06
rg_reciprocal	28.75 Å
i0_reciprocal	94160000.0000
total_estimate	0.6935
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	39.5 Å
skewness	0.114
kurtosis	-0.452
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	17580000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 1.000; Smooth: 0.987

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Sortilin
formula_weight	84991.2 kDa
mutation	V650M
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10547

MERPWGAADGLSRWPHGLGLLLLLQLLPPSTLSQDRLDAPPPPAAPLPRWSGPIGVSWGLRAAAAGGAFPRGGRWRRSAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPEKQNSKSNSHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Cricetulus griseus

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	;(2~{S})-2-[[6-[3-[8-[2-[(2~{R})-4-[5-[1-[(2-cyanopyridin-3-yl)methyl]-2,2-dimethyl-3-oxidanylidene-pyrrolo[2,3-b]pyridin-6-yl]pyrimidin-2-yl]-2-methyl-piperazin-1-yl]-2-oxidanylidene-ethoxy]octylcarbamoyl]phenoxy]pyridin-3-yl]carbonylamino]-5,5-dimethyl-hexanoic acid ;
formula_weight	1022.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	100

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6. Citations (1)

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length_a	161.771 Å
length_b	75.617 Å
length_c	110.197 Å
angle_alpha	90.00 °
angle_beta	127.39 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.802 Å
resolution_low	79.875 Å
r_factor	—
r_work	0.2119
r_free	0.2532

fit	/app/data/saxs_computation/r1/9r18/9r18.fit
pddf	/app/data/pr_computation/r1/9r18/9r18.pr.out
profile	/app/data/saxs_computation/r1/9r18/9r18.dat

Structure of Sortilin ECD in complex with TNFa-targeting SORTAC

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