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9u4s

Crystal Structure of PI5P4K-gamma in complex with n40

Method: X-RAY DIFFRACTION D_max: 116.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u4s
deposition_date	2025-03-20
title	Crystal Structure of PI5P4K-gamma in complex with n40
keywords	Kinase, Transferase, Lipid metabolism, LIPID BINDING PROTEIN; LIPID 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	33.08 Å
rg_electron	33.33 Å
i0	135202000.00
molecular_weight	62846.0 kDa
excluded_volume	61240 Å³
envelope_volume	113570 Å³
shell_volume	30733 Å³
envelope_diameter	115.9 Å
shell_rg	36.66 Å
envelope_rg	33.59 Å
shape_rg	33.31 Å
total_rg	33.57 Å
total_atoms	4776
n_residues	605
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	116.3 Å
rg_real	33.63 Å
rg_real_error	1.04 Å
i0_real	1.3520e+08
i0_real_error	2.2320e+06
rg_reciprocal	33.40 Å
i0_reciprocal	135200000.0000
total_estimate	0.5357
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	26.6 Å
skewness	0.590
kurtosis	-0.434
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	36090000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.506; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.432; Smooth: 0.863

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma
formula_weight	40205.9 kDa
ec_number	2.7.1.149
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4827

GHFVQQKVKVFRAADPLVGVFLWGVAHSINELSQVPPPVMLLPDDFKASSKIKVNNHLFHRENLPSHFKFKEYCPQVFRNLRDRFGIDDQDYLVSLTRNPPSESEGSDGRFLISYDRTLVIKEVSSEDIADMHSNLSNYHQYIVKCHGNTLLPQFLGMYRVSVDNEDSYMLVMRNMFSHRLPVHRKYDLKGSLVSREASDKEKVKELPTLKDMDFLNKNQKVYIGEEEKKIFLEKLKRDVEFLVQLKIMDYSLLLGIHDIIRGSEPEEELGPGEFESFIDVYAIRSAEGAPQKEVYFMGLIDILTQYDAKKKAAHAAKTVKHGAGAEISTVHPEQYAKRFLDFITNIFA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	~{N}-[5-(4-oxidanylidene-3-propyl-quinazolin-6-yl)pyridin-2-yl]pentanamide
formula_weight	364.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	51

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6. Citations (1)

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length_a	263.910 Å
length_b	47.760 Å
length_c	66.280 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 2 21
int_tables_number	18
crystal_system	—

resolution	2.250 Å
resolution_low	59.230 Å
r_factor	0.2800
r_work	0.2787
r_free	0.3036

fit	/app/data/saxs_computation/u4/9u4s/9u4s.fit
pddf	/app/data/pr_computation/u4/9u4s/9u4s.pr.out
profile	/app/data/saxs_computation/u4/9u4s/9u4s.dat

Crystal Structure of PI5P4K-gamma in complex with n40

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