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9t9w

Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide

Method: X-RAY DIFFRACTION D_max: 74.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t9w
deposition_date	2025-11-17
title	Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide
keywords	E3 ligase, phosphodegron, beta-TrCP, i-kappa-B-alpha, TRANSFERASE; TRANSFERASE
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	21.90 Å
rg_electron	21.08 Å
i0	32126300.00
molecular_weight	42310.0 kDa
excluded_volume	52410 Å³
envelope_volume	59931 Å³
shell_volume	23630 Å³
envelope_diameter	76.4 Å
shell_rg	27.99 Å
envelope_rg	21.34 Å
shape_rg	21.06 Å
total_rg	21.93 Å
total_atoms	2964
n_residues	363
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	74.2 Å
rg_real	21.83 Å
rg_real_error	0.46 Å
i0_real	3.2130e+07
i0_real_error	4.5190e+05
rg_reciprocal	21.85 Å
i0_reciprocal	32130000.0000
total_estimate	0.8749
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.6 Å
skewness	0.303
kurtosis	-0.244
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	11460000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	F-box/WD repeat-containing protein 1A
formula_weight	41829.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3332

GSGMEWKKEIERMVRTDSLWRGLAERRGWGQYLFKNKPPDGNAPPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCRSETSKGVYCLQYDDQKIVSGLRDNTIKIWDKNTLECKRILTGHTGSVLCLQYDERVIITGSSDSTVRVWDVNTGEMLNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMASPTDITLRRVLVGHRAAVNVVDFDDKYIVSASGDRTIKVWNTSTCEFVRTLNGHKRGIACLQYRDRLVVSGSSDNTIRLWDIECGACLRVLEGHEELVRCIRFDNKRIVSGAYDGKIKVWDLVAALDPRAPAGTLCLRTLVEHSGRVFRLQFDEFQIVSSSHDDTILIWDFLN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	NF-kappa-B inhibitor alpha
formula_weight	1538.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

DRHDSGLDSMKD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	338

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6. Citations (1)

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length_a	44.602 Å
length_b	46.822 Å
length_c	150.381 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.162 Å
resolution_low	23.130 Å
r_factor	0.1911
r_work	0.1899
r_free	0.2126

fit	/app/data/saxs_computation/t9/9t9w/9t9w.fit
pddf	/app/data/pr_computation/t9/9t9w/9t9w.pr.out
profile	/app/data/saxs_computation/t9/9t9w/9t9w.dat

Crystal structure of beta-TrCP bound by diphosphorylated I-kappa-B-alpha degron peptide

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)