← Back to search

9uk3

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

Method: X-RAY DIFFRACTION D_max: 52.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uk3
deposition_date	2025-04-17
title	Crystal structure of WDR5 in complex with peptide Ac-MRTEPRPPAP-NH2
keywords	WD repeat, WIN site, MLL complex, NUCLEAR PROTEIN; NUCLEAR PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	18.56 Å
rg_electron	17.60 Å
i0	18952700.00
molecular_weight	33844.0 kDa
excluded_volume	42487 Å³
envelope_volume	44784 Å³
shell_volume	20475 Å³
envelope_diameter	54.2 Å
shell_rg	24.64 Å
envelope_rg	17.74 Å
shape_rg	17.57 Å
total_rg	18.58 Å
total_atoms	2385
n_residues	311
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

▼

3. P(r) Analysis (GNOM)

dmax	52.9 Å
rg_real	18.40 Å
rg_real_error	0.23 Å
i0_real	1.8950e+07
i0_real_error	2.1190e+05
rg_reciprocal	18.42 Å
i0_reciprocal	18950000.0000
total_estimate	0.8350
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.4 Å
skewness	0.032
kurtosis	-0.543
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	6396000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	SCRIB overlapping open reading frame protein
formula_weight	1177.4 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	2716

XMRTEPRPPAPX

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	325

▶

6. Citations (1)

▶

length_a	41.072 Å
length_b	80.972 Å
length_c	84.539 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	1.690 Å
resolution_low	58.480 Å
r_factor	0.1699
r_work	0.1683
r_free	0.1995

fit	/app/data/saxs_computation/uk/9uk3/9uk3.fit
pddf	/app/data/pr_computation/uk/9uk3/9uk3.pr.out
profile	/app/data/saxs_computation/uk/9uk3/9uk3.dat

Crystal structure of WDR5 in complex with peptide Ac-MRTEPRPPAP-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

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)