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9uk1

Crystal structure of WDR5 in complex with EMBOW

Method: X-RAY DIFFRACTION D_max: 54.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uk1
deposition_date	2025-04-17
title	Crystal structure of WDR5 in complex with EMBOW
keywords	WD-repeat, WIN site, MLL complex, NUCLEAR PROTEIN; NUCLEAR 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	18.61 Å
rg_electron	17.64 Å
i0	18750800.00
molecular_weight	33609.0 kDa
excluded_volume	42195 Å³
envelope_volume	44870 Å³
shell_volume	20513 Å³
envelope_diameter	54.4 Å
shell_rg	24.59 Å
envelope_rg	17.74 Å
shape_rg	17.62 Å
total_rg	18.59 Å
total_atoms	2370
n_residues	310
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	54.5 Å
rg_real	18.45 Å
rg_real_error	0.16 Å
i0_real	1.8750e+07
i0_real_error	1.7080e+05
rg_reciprocal	18.48 Å
i0_reciprocal	18750000.0000
total_estimate	0.9075
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	24.6 Å
skewness	0.030
kurtosis	-0.541
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	6681000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.985

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	SCRIB overlapping open reading frame protein
formula_weight	12002.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	2533

MRTEPRPPAPSPPSAAAGARAAHPHHAQVHPAVALQPARGVGGQAALFAAGRAGGDLPLQPQPGGAAARRQPAARAAQAFFPAAELAQAGPERQRDPAVASRGGQLHAAGGAGRVPERYP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	WD repeat-containing protein 5
formula_weight	34391.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	163

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6. Citations (1)

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length_a	46.004 Å
length_b	81.043 Å
length_c	108.538 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	2.020 Å
resolution_low	46.000 Å
r_factor	0.1931
r_work	0.1914
r_free	0.2261

fit	/app/data/saxs_computation/uk/9uk1/9uk1.fit
pddf	/app/data/pr_computation/uk/9uk1/9uk1.pr.out
profile	/app/data/saxs_computation/uk/9uk1/9uk1.dat

Crystal structure of WDR5 in complex with EMBOW

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)