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9z2s

Structure of KIT V654A mutant with Compound 11

Method: X-RAY DIFFRACTION D_max: 66.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z2s
deposition_date	2025-11-05
title	Structure of KIT V654A mutant with Compound 11
keywords	Protein Kinase Inhibitor Kinase Complex Mutant, 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	20.57 Å
rg_electron	19.73 Å
i0	42121100.00
molecular_weight	34146.0 kDa
excluded_volume	33298 Å³
envelope_volume	53315 Å³
shell_volume	22167 Å³
envelope_diameter	69.7 Å
shell_rg	26.59 Å
envelope_rg	20.10 Å
shape_rg	19.70 Å
total_rg	20.44 Å
total_atoms	2578
n_residues	318
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	66.4 Å
rg_real	20.48 Å
rg_real_error	0.40 Å
i0_real	4.2120e+07
i0_real_error	5.3820e+05
rg_reciprocal	20.50 Å
i0_reciprocal	42120000.0000
total_estimate	0.8150
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.0 Å
skewness	0.220
kurtosis	-0.412
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	10340000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Mast/stem cell growth factor receptor
formula_weight	41163.3 kDa
ec_number	2.7.10.1
mutation	V654A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3055

MSYYHHHHHHDYDIPTTENLYFQGPTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIANLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	6-[(6-amino-2-cyclopropylpyrimidin-4-yl)amino]-N-methyl-4-[(propan-2-yl)amino]pyridine-3-carboxamide
formula_weight	341.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	452

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6. Citations (1)

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length_a	47.682 Å
length_b	79.906 Å
length_c	92.240 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.100 Å
resolution_low	29.080 Å
r_factor	0.1697
r_work	0.1665
r_free	0.2299

fit	/app/data/saxs_computation/z2/9z2s/9z2s.fit
pddf	/app/data/pr_computation/z2/9z2s/9z2s.pr.out
profile	/app/data/saxs_computation/z2/9z2s/9z2s.dat