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9y4q

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102

Method: X-RAY DIFFRACTION D_max: 88.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y4q
deposition_date	2025-09-03
last_revision	2026-01-14
title	Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102
keywords	WD-repeat, WDR, DCAF1, SGC, 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	27.19 Å
rg_electron	26.49 Å
i0	141082000.00
molecular_weight	62677.0 kDa
excluded_volume	60533 Å³
envelope_volume	99435 Å³
shell_volume	31433 Å³
envelope_diameter	93.6 Å
shell_rg	33.72 Å
envelope_rg	26.33 Å
shape_rg	26.45 Å
total_rg	27.10 Å
total_atoms	4724
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	88.1 Å
rg_real	27.19 Å
rg_real_error	0.63 Å
i0_real	1.4110e+08
i0_real_error	1.7440e+06
rg_reciprocal	27.19 Å
i0_reciprocal	141100000.0000
total_estimate	0.8989
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	86.6 Å
skewness	0.318
kurtosis	-0.511
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	21930000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	5305

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-(pyrimidin-5-yl)-1H-pyrrole-3-carboxamide ;
formula_weight	516.3 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	455

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6. Citations (1)

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length_a	48.692 Å
length_b	88.192 Å
length_c	73.099 Å
angle_alpha	90.00 °
angle_beta	97.47 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.480 Å
resolution_low	38.000 Å
r_factor	0.1595
r_work	0.1578
r_free	0.1932

fit	/app/data/saxs_computation/y4/9y4q/9y4q.fit
pddf	/app/data/pr_computation/y4/9y4q/9y4q.pr.out
profile	/app/data/saxs_computation/y4/9y4q/9y4q.dat

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102

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