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11mm

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-81

Method: X-RAY DIFFRACTION D_max: 85.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11mm
deposition_date	2026-03-05
last_revision	2026-03-18
title	The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-81
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	25.99 Å
rg_electron	25.11 Å
i0	114228000.00
molecular_weight	56492.0 kDa
excluded_volume	54808 Å³
envelope_volume	90827 Å³
shell_volume	30112 Å³
envelope_diameter	87.2 Å
shell_rg	32.46 Å
envelope_rg	25.33 Å
shape_rg	25.09 Å
total_rg	25.75 Å
total_atoms	4286
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	85.8 Å
rg_real	25.92 Å
rg_real_error	0.51 Å
i0_real	1.1420e+08
i0_real_error	1.5790e+06
rg_reciprocal	25.95 Å
i0_reciprocal	114200000.0000
total_estimate	0.8934
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.0 Å
skewness	0.257
kurtosis	-0.419
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	19020000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	A
atom_count	4353

MGHHHHHHHHHHAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF

Source

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

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(8S)-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]pyrazolo[1,5-a]pyrimidine
formula_weight	294.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	21

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6. Citations (1)

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length_a	114.448 Å
length_b	114.448 Å
length_c	145.847 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	2.690 Å
resolution_low	53.270 Å
r_factor	0.2076
r_work	0.2048
r_free	0.2646

fit	/app/data/saxs_computation/1m/11mm/11mm.fit
pddf	/app/data/pr_computation/1m/11mm/11mm.pr.out
profile	/app/data/saxs_computation/1m/11mm/11mm.dat