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9z5q

HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11

Method: ELECTRON MICROSCOPY D_max: 88.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z5q
deposition_date	2025-11-12
title	HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11
keywords	Ubiquitin, targeted protein degradation, E3 ligase, Nanobody, LIGASE; LIGASE
method	ELECTRON MICROSCOPY

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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	27.83 Å
rg_electron	26.75 Å
i0	62913900.00
molecular_weight	62719.0 kDa
excluded_volume	78694 Å³
envelope_volume	96485 Å³
shell_volume	30344 Å³
envelope_diameter	95.5 Å
shell_rg	33.69 Å
envelope_rg	26.58 Å
shape_rg	26.75 Å
total_rg	27.51 Å
total_atoms	8716
n_residues	539
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	88.8 Å
rg_real	27.71 Å
rg_real_error	0.51 Å
i0_real	6.2910e+07
i0_real_error	9.0130e+05
rg_reciprocal	27.75 Å
i0_reciprocal	62920000.0000
total_estimate	0.9061
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.4 Å
skewness	0.160
kurtosis	-0.541
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	15100000.0000
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: 0.999; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Nanobody C11 (nb.C11)
formula_weight	17817.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8716

MKYLLPTAAAGLLLLAAQPAMAMDIGINSDPQVQLQESGGGLVQAGGSLRLSCAASGNISDVWYMGWYRQAPGKEREFVAGIAYGTSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVIITRFVSYPRQHTYWGQGTQVTVSSPLEHHHHHH

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	E3 ubiquitin-protein ligase NEDD4-like
formula_weight	52598.5 kDa
ec_number	2.3.2.26,2.3.2.36
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SYSLNPNDLGPLPPGWEERIHLDGRTFYIDHNSKITQWEDPRLQNPAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSPEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVDMDYKDDDDK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.060 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.06 Å
resolution_method	—
num_particles	90979

fit	/app/data/saxs_computation/z5/9z5q/9z5q.fit
pddf	/app/data/pr_computation/z5/9z5q/9z5q.pr.out
profile	/app/data/saxs_computation/z5/9z5q/9z5q.dat

HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)