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9q33

Cereblon Ternary Complex with Blimp1 and compound 5

Method: ELECTRON MICROSCOPY D_max: 103.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q33
deposition_date	2025-08-15
title	Cereblon Ternary Complex with Blimp1 and compound 5
keywords	Liganded Cereblon Ligase Substrate, LIGASE; LIGASE
method	ELECTRON MICROSCOPY

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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	27.82 Å
rg_electron	27.44 Å
i0	121096000.00
molecular_weight	58244.0 kDa
excluded_volume	56339 Å³
envelope_volume	99934 Å³
shell_volume	31455 Å³
envelope_diameter	111.8 Å
shell_rg	33.41 Å
envelope_rg	28.08 Å
shape_rg	27.43 Å
total_rg	27.91 Å
total_atoms	4397
n_residues	536
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	103.7 Å
rg_real	28.03 Å
rg_real_error	0.97 Å
i0_real	1.2110e+08
i0_real_error	1.8160e+06
rg_reciprocal	27.96 Å
i0_reciprocal	121100000.0000
total_estimate	0.8064
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.9 Å
skewness	0.635
kurtosis	0.303
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	21190000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.577; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.905

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PR domain zinc finger protein 1
formula_weight	21865.5 kDa
ec_number	2.1.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4397

GSKMDMEDADMTLWTEAEFEEKCTYIVNDHPWDSGADGGTSVQAEASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRIYSRGELHHFIDGFNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNLTQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

description	Protein cereblon
formula_weight	50603.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	;N-({(4R)-7-[(1S)-2-amino-1-(4-bromo-2-methylphenyl)-2-oxoethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyrazin-3-yl}methyl)-13-{4-[(3R)-2,6-dioxopiperidin-3-yl]anilino}tridecanamide ;
formula_weight	776.8 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	174443

fit	/app/data/saxs_computation/q3/9q33/9q33.fit
pddf	/app/data/pr_computation/q3/9q33/9q33.pr.out
profile	/app/data/saxs_computation/q3/9q33/9q33.dat

Cereblon Ternary Complex with Blimp1 and compound 5

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)