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9z1l

Structure of KIT V654A mutant with Compound 1

Method: X-RAY DIFFRACTION D_max: 69.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z1l
deposition_date	2025-11-04
title	Structure of KIT V654A mutant with Compound 1
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	20.67 Å
rg_electron	19.83 Å
i0	40314800.00
molecular_weight	33406.0 kDa
excluded_volume	32610 Å³
envelope_volume	52725 Å³
shell_volume	21933 Å³
envelope_diameter	68.4 Å
shell_rg	26.51 Å
envelope_rg	20.21 Å
shape_rg	19.80 Å
total_rg	20.54 Å
total_atoms	2528
n_residues	312
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	69.3 Å
rg_real	20.59 Å
rg_real_error	0.38 Å
i0_real	4.0310e+07
i0_real_error	4.7740e+05
rg_reciprocal	20.60 Å
i0_reciprocal	40320000.0000
total_estimate	0.6284
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	68.3 Å
skewness	0.245
kurtosis	-0.403
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	9764000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	3104

MSYYHHHHHHDYDIPTTENLYFQGPTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIANLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHI

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	(4R)-2-METHYLPENTANE-2,4-DIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	N~2~-methyl-N~4~-{(5P)-5-(1-methyl-1H-pyrazol-4-yl)-4-[(propan-2-yl)oxy]pyridin-2-yl}pyrimidine-2,4-diamine
formula_weight	339.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	488

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6. Citations (1)

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length_a	56.300 Å
length_b	56.300 Å
length_c	202.722 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.543 Å
resolution_low	54.247 Å
r_factor	—
r_work	0.1646
r_free	0.2062

fit	/app/data/saxs_computation/z1/9z1l/9z1l.fit
pddf	/app/data/pr_computation/z1/9z1l/9z1l.pr.out
profile	/app/data/saxs_computation/z1/9z1l/9z1l.dat

Structure of KIT V654A mutant with Compound 1

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