SAXSdb — 9qe5

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1. Structure Basics

entry_id	9qe5
deposition_date	2025-03-07
title	VCB in complex with VHL-binding compound 82
keywords	protac, degrader, complex, e3 ligase, vhl, vcb, ligase; LIGASE
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	41.24 Å
rg_electron	41.00 Å
i0	686387000.00
molecular_weight	142690.0 kDa
excluded_volume	138070 Å³
envelope_volume	273070 Å³
shell_volume	57279 Å³
envelope_diameter	138.6 Å
shell_rg	44.84 Å
envelope_rg	40.06 Å
shape_rg	41.03 Å
total_rg	41.11 Å
total_atoms	10779
n_residues	1335
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	134.0 Å
rg_real	41.19 Å
rg_real_error	0.96 Å
i0_real	6.8640e+08
i0_real_error	1.1840e+07
rg_reciprocal	41.24 Å
i0_reciprocal	686400000.0000
total_estimate	0.8820
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.4 Å
skewness	0.276
kurtosis	-0.361
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	20630000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.749

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Elongin-B
formula_weight	14914.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,G,J
atom_count	10783

MKHHHHHHPMSDYDIPTTENLYFQGMDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Elongin-C
formula_weight	10974.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,E,H,K

MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	von Hippel-Lindau disease tumor suppressor
formula_weight	23116.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,F,I,L

MASAWSHPQFEKGGGSGGGSGGSAWSHPQFEKSGENLYFQGSHMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

description	;(2~{S},4~{R})-1-[(2~{S})-1-(1-fluoranylcyclopropyl)carbonylpiperidin-2-yl]carbonyl-~{N}-[(1~{S})-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide ;
formula_weight	528.6 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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6. Citations (1)

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length_a	94.215 Å
length_b	94.215 Å
length_c	366.025 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 41 2 2
int_tables_number	91
crystal_system	tetragonal

resolution	2.500 Å
resolution_low	45.720 Å
r_factor	0.2460
r_work	0.2452
r_free	0.2726

fit	/app/data/saxs_computation/qe/9qe5/9qe5.fit
pddf	/app/data/pr_computation/qe/9qe5/9qe5.pr.out
profile	/app/data/saxs_computation/qe/9qe5/9qe5.dat

VCB in complex with VHL-binding compound 82

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)