SAXSdb — 9z1l

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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	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

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 9Z1L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Z2S Structure of KIT V654A mutant with Compound 11 Deposited 2025-11-05	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	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

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	9z1l
Deposition date deposition_date	2025-11-04
Structure title title	Structure of KIT V654A mutant with Compound 1
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	20.67 Å
Radius of gyration Rg (electron density) rg_electron	19.83 Å
Forward intensity I(0) i0	40314800.00
Molecular weight molecular_weight	33406.0 kDa
Excluded volume excluded_volume	32610 Å³
Envelope volume envelope_volume	52725 Å³
Hydration-shell volume shell_volume	21933 Å³
Envelope diameter envelope_diameter	68.4 Å
Shell Rg shell_rg	26.51 Å
Envelope Rg envelope_rg	20.21 Å
Shape Rg shape_rg	19.80 Å
Total Rg total_rg	20.54 Å
Total atoms total_atoms	2528
Residues n_residues	312
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	69.3 Å
Rg (real space) rg_real	20.59 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	4.0310e+07
I(0) uncertainty (real space) i0_real_error	4.7740e+05
Rg (reciprocal space) rg_reciprocal	20.60 Å
I(0) (reciprocal space) i0_reciprocal	40320000.0000
Solution quality estimate total_estimate	0.6284
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	68.3 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.403
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9764000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	3104

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	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description 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
Molecular weight formula_weight	339.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	488

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8. Citations (1)

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Unit-cell length a length_a	56.300 Å
Unit-cell length b length_b	56.300 Å
Unit-cell length c length_c	202.722 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.543 Å
Low-resolution limit resolution_low	54.247 Å
R factor r_factor	—
R_work r_work	0.1646
R_free 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

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