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9y7d

Cereblon with Golcadomide and Ikaros ZF1-2-3

Method: ELECTRON MICROSCOPY D_max: 85.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y7d
deposition_date	2025-09-09
title	Cereblon with Golcadomide and Ikaros ZF1-2-3
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	24.41 Å
rg_electron	23.72 Å
i0	65907100.00
molecular_weight	42213.0 kDa
excluded_volume	40758 Å³
envelope_volume	72517 Å³
shell_volume	25968 Å³
envelope_diameter	89.3 Å
shell_rg	30.33 Å
envelope_rg	24.03 Å
shape_rg	23.70 Å
total_rg	24.34 Å
total_atoms	3183
n_residues	405
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	85.8 Å
rg_real	24.42 Å
rg_real_error	0.62 Å
i0_real	6.5910e+07
i0_real_error	1.0500e+06
rg_reciprocal	24.42 Å
i0_reciprocal	65910000.0000
total_estimate	0.6889
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.397
kurtosis	-0.163
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	12170000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 0.264; Positv: 1.000; Valcen: 0.923; Smooth: 0.971

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein cereblon
formula_weight	46596.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	3183

GSMEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	DNA-binding protein Ikaros
formula_weight	12605.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GRMLDASGEKMNGSHRDQGSSALSGVGGIRLPNGKLKCDICGIICIGPNVLMVHKRSHTGERPFQCNQCGASFTQKGNLLRHIKLHSGEKPFKCHLCNYACRRRDALTGHLRTHS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	Golcadomide
formula_weight	535.6 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	3.26 Å
resolution_method	—
num_particles	170954

fit	/app/data/saxs_computation/y7/9y7d/9y7d.fit
pddf	/app/data/pr_computation/y7/9y7d/9y7d.pr.out
profile	/app/data/saxs_computation/y7/9y7d/9y7d.dat

Cereblon with Golcadomide and Ikaros ZF1-2-3

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

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)