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9ujz

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

Method: X-RAY DIFFRACTION D_max: 60.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ujz
deposition_date	2025-04-17
title	Crystal structure of WDR5 in complex with peptide Ac-MRTEPRP-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	18.59 Å
rg_electron	17.60 Å
i0	18637300.00
molecular_weight	33388.0 kDa
excluded_volume	41933 Å³
envelope_volume	44693 Å³
shell_volume	20425 Å³
envelope_diameter	56.4 Å
shell_rg	24.74 Å
envelope_rg	17.79 Å
shape_rg	17.57 Å
total_rg	18.64 Å
total_atoms	2354
n_residues	307
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	60.3 Å
rg_real	18.44 Å
rg_real_error	0.27 Å
i0_real	1.8640e+07
i0_real_error	2.3040e+05
rg_reciprocal	18.46 Å
i0_reciprocal	18640000.0000
total_estimate	0.8028
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.8 Å
skewness	0.054
kurtosis	-0.511
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	7369000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; 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	2448

SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	ACE-MET-ARG-THR-GLU-PRO-ARG-PRO-NH2
formula_weight	912.1 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

XMRTEPRPX

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	94

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6. Citations (1)

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length_a	77.560 Å
length_b	99.050 Å
length_c	80.500 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	2.460 Å
resolution_low	48.650 Å
r_factor	0.1743
r_work	0.1714
r_free	0.2287

fit	/app/data/saxs_computation/uj/9ujz/9ujz.fit
pddf	/app/data/pr_computation/uj/9ujz/9ujz.pr.out
profile	/app/data/saxs_computation/uj/9ujz/9ujz.dat

Crystal structure of WDR5 in complex with peptide Ac-MRTEPRP-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)