SAXSdb — 9q22

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1. Structure Basics

entry_id	9q22
deposition_date	2025-08-14
title	Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1
keywords	CEREBLON, DEGRADER, HELIOS, IKZF2, DDB1, MOCLECULAR GLUE, 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	34.62 Å
rg_electron	33.78 Å
i0	276751000.00
molecular_weight	134170.0 kDa
excluded_volume	167800 Å³
envelope_volume	212710 Å³
shell_volume	51486 Å³
envelope_diameter	118.5 Å
shell_rg	41.10 Å
envelope_rg	33.81 Å
shape_rg	33.70 Å
total_rg	34.57 Å
total_atoms	18612
n_residues	1209
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	110.7 Å
rg_real	34.53 Å
rg_real_error	0.78 Å
i0_real	2.7680e+08
i0_real_error	4.6550e+06
rg_reciprocal	34.58 Å
i0_reciprocal	276800000.0000
total_estimate	0.8986
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	108.3 Å
skewness	0.257
kurtosis	-0.451
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	78010000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.943

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DNA damage-binding protein 1
formula_weight	95773.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	18612

MHHHHHHVDEENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Protein cereblon
formula_weight	48976.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDWSHPQFEKSAVDENLYFQGGGRAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Zinc finger protein Helios
formula_weight	3431.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GSTGERPFHCNQCGASFTQKGNLLRHIKLHS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	(3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
formula_weight	433.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	260.240 Å
length_b	260.240 Å
length_c	123.660 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	3.406 Å
resolution_low	130.120 Å
r_factor	0.2218
r_work	0.2203
r_free	0.2520

fit	/app/data/saxs_computation/q2/9q22/9q22.fit
pddf	/app/data/pr_computation/q2/9q22/9q22.pr.out
profile	/app/data/saxs_computation/q2/9q22/9q22.dat

Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)