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9zf4

The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83

Method: X-RAY DIFFRACTION D_max: 82.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zf4
deposition_date	2025-12-01
last_revision	2026-04-22
title	The structure of human Vacuolar Protein Sorting 34 catalytic domain bound to RD-II-83
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	26.28 Å
rg_electron	24.93 Å
i0	59405200.00
molecular_weight	61701.0 kDa
excluded_volume	77944 Å³
envelope_volume	91355 Å³
shell_volume	30367 Å³
envelope_diameter	85.7 Å
shell_rg	32.46 Å
envelope_rg	25.13 Å
shape_rg	24.81 Å
total_rg	26.19 Å
total_atoms	8672
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	82.8 Å
rg_real	26.18 Å
rg_real_error	0.55 Å
i0_real	5.9410e+07
i0_real_error	9.1400e+05
rg_reciprocal	26.22 Å
i0_reciprocal	59410000.0000
total_estimate	0.9061
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.3 Å
skewness	0.226
kurtosis	-0.447
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	14900000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

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	8956

MGHHHHHHHHHHAATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHALF

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	methyl 2-[(8R)-pyrazolo[1,5-a]pyrimidin-3-yl]-1,3-benzothiazole-6-carboxylate
formula_weight	310.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 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	5

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	163

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6. Citations (1)

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length_a	113.074 Å
length_b	113.074 Å
length_c	145.461 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	2.090 Å
resolution_low	61.170 Å
r_factor	0.1934
r_work	0.1917
r_free	0.2237

fit	/app/data/saxs_computation/zf/9zf4/9zf4.fit
pddf	/app/data/pr_computation/zf/9zf4/9zf4.pr.out
profile	/app/data/saxs_computation/zf/9zf4/9zf4.dat