SAXSdb — 9z2s

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mast/stem cell growth factor receptor

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 540–930	Mutation：V654A	DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 3 A1CZ3 6-[(6-amino-2-cyclopropylpyrimidin-4-yl)amino]-N-methyl-4-[(propan-2-yl)amino]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；8% PEG 4000 0.1 M HEPES, pH 8.2	Resolution 2.10 Å R-free 0.230

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9Z2S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Z1L Structure of KIT V654A mutant with Compound 1 Deposited 2025-11-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 540–930（391 aa）	Mutation：V654A	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 A1CZZ 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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；285 K；10% 2-propanol, 100 mM Na-Citrate pH 5.0, 8% PEG 4000	Resolution 1.54 Å R-free 0.206

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0U2N547_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–359； UniProt 540–930

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z2s
Deposition date deposition_date	2025-11-05
Structure title title	Structure of KIT V654A mutant with Compound 11
Keywords keywords	Protein Kinase Inhibitor Kinase Complex Mutant, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.57 Å
Radius of gyration Rg (electron density) rg_electron	19.73 Å
Forward intensity I(0) i0	42121100.00
Molecular weight molecular_weight	34146.0 kDa
Excluded volume excluded_volume	33298 Å³
Envelope volume envelope_volume	53315 Å³
Hydration-shell volume shell_volume	22167 Å³
Envelope diameter envelope_diameter	69.7 Å
Shell Rg shell_rg	26.59 Å
Envelope Rg envelope_rg	20.10 Å
Shape Rg shape_rg	19.70 Å
Total Rg total_rg	20.44 Å
Total atoms total_atoms	2578
Residues n_residues	318
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.4 Å
Rg (real space) rg_real	20.48 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	4.2120e+07
I(0) uncertainty (real space) i0_real_error	5.3820e+05
Rg (reciprocal space) rg_reciprocal	20.50 Å
I(0) (reciprocal space) i0_reciprocal	42120000.0000
Solution quality estimate total_estimate	0.8150
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.220
Kurtosis Kurtosis kurtosis	-0.412
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10340000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Mast/stem cell growth factor receptor
Molecular weight formula_weight	41163.3 kDa
EC 编号 ec_number	2.7.10.1
Mutation mutation	V654A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3055

MSYYHHHHHHDYDIPTTENLYFQGPTYKYLQKPMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIANLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	6-[(6-amino-2-cyclopropylpyrimidin-4-yl)amino]-N-methyl-4-[(propan-2-yl)amino]pyridine-3-carboxamide
Molecular weight formula_weight	341.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	452

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8. Citations (1)

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Unit-cell length a length_a	47.682 Å
Unit-cell length b length_b	79.906 Å
Unit-cell length c length_c	92.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.080 Å
R factor r_factor	0.1697
R_work r_work	0.1665
R_free 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

Structure of KIT V654A mutant with Compound 11

1. Protein Identity and Related Structures Protein Identity & Related Structures

Mast/stem cell growth factor receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction