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9ydg

Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074

Method: X-RAY DIFFRACTION D_max: 89.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ydg
deposition_date	2025-09-22
last_revision	2025-11-12
title	Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074
keywords	;WD-repeat, WDR, DCAF1, SGC, Structural Genomics, PSI-2, Protein Structure Initiative, Structural Genomics Consortium, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
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	27.28 Å
rg_electron	26.58 Å
i0	139034000.00
molecular_weight	62393.0 kDa
excluded_volume	60327 Å³
envelope_volume	99716 Å³
shell_volume	31447 Å³
envelope_diameter	93.8 Å
shell_rg	33.86 Å
envelope_rg	26.36 Å
shape_rg	26.54 Å
total_rg	27.18 Å
total_atoms	4701
n_residues	595
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	89.3 Å
rg_real	27.28 Å
rg_real_error	0.81 Å
i0_real	1.3900e+08
i0_real_error	2.0950e+06
rg_reciprocal	27.28 Å
i0_reciprocal	139000000.0000
total_estimate	0.8941
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.324
kurtosis	-0.509
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	23250000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	DDB1- and CUL4-associated factor 1
formula_weight	35592.9 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5245

GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	;(4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide ;
formula_weight	577.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

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

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	397

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6. Citations (1)

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length_a	49.067 Å
length_b	87.819 Å
length_c	73.680 Å
angle_alpha	90.00 °
angle_beta	98.27 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.540 Å
resolution_low	48.600 Å
r_factor	0.1896
r_work	0.1881
r_free	0.2179

fit	/app/data/saxs_computation/yd/9ydg/9ydg.fit
pddf	/app/data/pr_computation/yd/9ydg/9ydg.pr.out
profile	/app/data/saxs_computation/yd/9ydg/9ydg.dat