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10tc

Structure of WDR5 bound to RbBP5 (D376N)

Method: X-RAY DIFFRACTION D_max: 115.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10tc
deposition_date	2026-02-07
last_revision	2026-05-20
title	Structure of WDR5 bound to RbBP5 (D376N)
keywords	histone, epigenetic, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING 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	36.09 Å
rg_electron	35.57 Å
i0	268848000.00
molecular_weight	134670.0 kDa
excluded_volume	169170 Å³
envelope_volume	206330 Å³
shell_volume	48087 Å³
envelope_diameter	118.0 Å
shell_rg	42.24 Å
envelope_rg	35.03 Å
shape_rg	35.56 Å
total_rg	36.05 Å
total_atoms	9493
n_residues	1242
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	115.2 Å
rg_real	35.99 Å
rg_real_error	0.73 Å
i0_real	2.6880e+08
i0_real_error	4.3380e+06
rg_reciprocal	36.06 Å
i0_reciprocal	268900000.0000
total_estimate	0.9005
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	52.4 Å
skewness	0.149
kurtosis	-0.662
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	97190000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.913

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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	33492.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,C,E,G
atom_count	10074

VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	RbBP5
formula_weight	910.0 kDa
src_method	syn
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,D,F,H

EVNVTSVY

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	565

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6. Citations (1)

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length_a	78.480 Å
length_b	105.711 Å
length_c	80.513 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.200 Å
resolution_low	26.430 Å
r_factor	0.1877
r_work	0.1848
r_free	0.2433

fit	/app/data/saxs_computation/0t/10tc/10tc.fit
pddf	/app/data/pr_computation/0t/10tc/10tc.pr.out
profile	/app/data/saxs_computation/0t/10tc/10tc.dat

Structure of WDR5 bound to RbBP5 (D376N)

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)