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9vn5

Structure of WDR5 in complex with MBD3C R43K

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vn5
deposition_date	2025-06-30
title	Structure of WDR5 in complex with MBD3C R43K
keywords	WDR5, MBD3C, WIN motif, chromatin, 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	27.68 Å
rg_electron	26.95 Å
i0	74222000.00
molecular_weight	68624.0 kDa
excluded_volume	86291 Å³
envelope_volume	99465 Å³
shell_volume	30979 Å³
envelope_diameter	88.1 Å
shell_rg	34.14 Å
envelope_rg	26.69 Å
shape_rg	26.93 Å
total_rg	27.77 Å
total_atoms	4834
n_residues	628
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	85.0 Å
rg_real	27.71 Å
rg_real_error	0.60 Å
i0_real	7.4220e+07
i0_real_error	1.0660e+06
rg_reciprocal	27.71 Å
i0_reciprocal	74220000.0000
total_estimate	0.8938
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.325
kurtosis	-0.622
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	19900000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.846

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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	34646.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5056

GSHMTQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Methyl-CpG binding domain protein 3
formula_weight	1037.2 kDa
mutation	R79K
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

GAAKCRVFSP

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	210

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6. Citations (1)

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length_a	116.265 Å
length_b	47.376 Å
length_c	129.472 Å
angle_alpha	90.00 °
angle_beta	113.34 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.900 Å
resolution_low	43.300 Å
r_factor	0.2065
r_work	0.2052
r_free	0.2311

fit	/app/data/saxs_computation/vn/9vn5/9vn5.fit
pddf	/app/data/pr_computation/vn/9vn5/9vn5.pr.out
profile	/app/data/saxs_computation/vn/9vn5/9vn5.dat

Structure of WDR5 in complex with MBD3C R43K

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)