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9uk4

Crystal structure of WDR5 in complex with peptide Ac-ARA-NH2

Method: X-RAY DIFFRACTION D_max: 57.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uk4
deposition_date	2025-04-17
title	Crystal structure of WDR5 in complex with peptide Ac-ARA-NH2
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	18.47 Å
rg_electron	17.54 Å
i0	17920100.00
molecular_weight	32973.0 kDa
excluded_volume	41445 Å³
envelope_volume	43897 Å³
shell_volume	20191 Å³
envelope_diameter	55.9 Å
shell_rg	24.55 Å
envelope_rg	17.67 Å
shape_rg	17.51 Å
total_rg	18.51 Å
total_atoms	2326
n_residues	304
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	57.5 Å
rg_real	18.32 Å
rg_real_error	0.20 Å
i0_real	1.7920e+07
i0_real_error	1.8890e+05
rg_reciprocal	18.34 Å
i0_reciprocal	17920000.0000
total_estimate	0.8165
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.041
kurtosis	-0.525
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	5727000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 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
atom_count	2399

SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	ACE-ALA-ARG-ALA-NH2
formula_weight	341.4 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

XARAX

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	73

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6. Citations (1)

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length_a	77.830 Å
length_b	99.050 Å
length_c	80.270 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.120 Å
resolution_low	48.670 Å
r_factor	0.2028
r_work	0.2005
r_free	0.2423

fit	/app/data/saxs_computation/uk/9uk4/9uk4.fit
pddf	/app/data/pr_computation/uk/9uk4/9uk4.pr.out
profile	/app/data/saxs_computation/uk/9uk4/9uk4.dat

Crystal structure of WDR5 in complex with peptide Ac-ARA-NH2

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

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)