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11yc

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123

Method: X-RAY DIFFRACTION D_max: 83.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11yc
deposition_date	2026-03-17
last_revision	2026-03-25
title	The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-123
keywords	Phosphatidylinositol 3-phosphate, lipid regulator, autophagy, membrane trafficking, endocytosis, enzyme, TRANSFERASE; TRANSFERASE
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	26.07 Å
rg_electron	25.20 Å
i0	114622000.00
molecular_weight	56757.0 kDa
excluded_volume	55179 Å³
envelope_volume	91356 Å³
shell_volume	30235 Å³
envelope_diameter	86.7 Å
shell_rg	32.50 Å
envelope_rg	25.31 Å
shape_rg	25.14 Å
total_rg	25.89 Å
total_atoms	4308
n_residues	536
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	83.3 Å
rg_real	25.99 Å
rg_real_error	0.52 Å
i0_real	1.1460e+08
i0_real_error	1.6850e+06
rg_reciprocal	26.01 Å
i0_reciprocal	114600000.0000
total_estimate	0.7227
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.4 Å
skewness	0.248
kurtosis	-0.436
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	19160000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 0.221; Positv: 1.000; Valcen: 1.000; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phosphatidylinositol 3-kinase catalytic subunit type 3
formula_weight	68149.9 kDa
ec_number	2.7.1.137
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	4365

MGHHHHHHHHHHAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF

Source

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

Entity 2 non-polymer

description	(8S)-3-(6-butyl-1,3-benzothiazol-2-yl)pyrazolo[1,5-a]pyrimidine
formula_weight	308.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	35

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6. Citations (1)

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length_a	114.253 Å
length_b	114.253 Å
length_c	146.029 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	2.410 Å
resolution_low	57.130 Å
r_factor	0.1950
r_work	0.1938
r_free	0.2195

fit	/app/data/saxs_computation/1y/11yc/11yc.fit
pddf	/app/data/pr_computation/1y/11yc/11yc.pr.out
profile	/app/data/saxs_computation/1y/11yc/11yc.dat