SAXSdb — 6joj

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

Platelet-derived growth factor receptor alpha

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 550–696 Chain A； UniProt 769–973	Not recorded	6T2 1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH6.9, 1.6M (NH4)2SO4, 0.1M NaCl	Resolution 2.60 Å R-free 0.233

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 6JOJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5GRN Crystal structure of PDGFRA in Complex with WQ-C-159 Deposited 2016-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Fragment：UNP residues 550-696 and 769-973 Chain A 769–973（205 aa） Fragment：UNP residues 550-696 and 769-973	Not recorded	748 N-[2-(dimethylamino)ethyl]-N-[[4-[[4-methyl-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]carbamoyl]phenyl]methyl]pyridine-3-carboxamide × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M KCl, 20% PEG 3350, pH 7.0	Resolution 1.77 Å R-free 0.179
5K5X Crystal structure of human PDGFRA Deposited 2016-05-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Fragment：UNP residues 550-696,769-973 Chain A 769–973（205 aa） Fragment：UNP residues 550-696,769-973	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M HEPES pH7.5, 1.6M (NH4)2SO4, 0.1M NaCl	Resolution 2.17 Å R-free 0.224
6A32 Crystal structure of PDGFRA kinase domain mutant T674I Deposited 2018-06-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris pH 5.5, 27% PEG 3350	Resolution 1.87 Å R-free 0.240
6JOI Crystal structure of PDGFRA T674I in complex with crenolanib by co-crystallization Deposited 2019-03-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	6T2 1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M NaCl, 0.1M Tris pH 8.0, 15% PEG 4000	Resolution 3.10 Å R-free 0.244
6JOK Crystal structure of PDGFRA in complex with sunitinib by soaking Deposited 2019-03-22	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	B49 N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH6.9, 1.6M (NH4)2SO4, 0.1M NaCl	Resolution 3.80 Å R-free 0.282
6JOL Crystal structure of PDGFRA in complex with imatinib by co-crystallization Deposited 2019-03-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Sodium citrate pH4.5, 20% PEG 4000	Resolution 1.90 Å R-free 0.236
7LBF CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109 Deposited 2021-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain D 1–524（524 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；The sample was gently cross-linked with 0.025% (v/v) EM-grade glutaraldehyde for 10 min at RT and quenched with 9 mM Tris pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 seconds before plunging	Resolution 2.80 Å
7RAM Cryo-EM Structure of the HCMV gHgLgO Trimer Derived from AD169 and TR strains in complex with PDGFRalpha Deposited 2021-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–524（524 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；300mM NaCl and 20mM HEPES7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
8PQH PDGFRA T674I mutant kinase domain in complex with avapritinib Deposited 2023-07-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	9JI Avapritinib × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；10 mg/mL, 13% PEG3350, 200 mM KCl	Resolution 2.50 Å R-free 0.249
8PQI PDGFRA T674I mutant kinase domain in complex with avapritinib derivative 9 Deposited 2023-07-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	9OO (1~{S})-~{N}-ethyl-1-(4-fluorophenyl)-1-[2-[4-[6-(1-methylpyrazol-4-yl)pyrrolo[2,1-f][1,2,4]triazin-4-yl]piperazin-1-yl]pyrimidin-5-yl]ethanamine × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；5 mg/mL, 5% PEG3350, 200 mM KCl	Resolution 2.60 Å R-free 0.254
8PQJ PDGFRA wild-type kinase domain Deposited 2023-07-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；285.15 K；10 mg/mL, 15% PEG3350, 100 mM Bis-Tris-Propane, pH 7.5	Resolution 1.82 Å R-free 0.215
8PQK APO crystal structure of PDGFRA-T674I kinase domain Deposited 2023-07-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–696（147 aa） Chain A 769–973（205 aa）	Mutation：T674I Mutation：T674I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；10 mg/mL, 22% PEG3350, 100 mM Bis-Tris-Propane, pH 7.5	Resolution 2.00 Å R-free 0.222
9GZH PDGFRA-T674I in complex with covalent ponatinib derivative 19 Deposited 2024-10-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 550–973（424 aa）	Mutation：T674I	A1IRC 3-(2-imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-~{N}-[4-(propanoylamino)-3-(trifluoromethyl)phenyl]benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；5 mg/mL, 18% PEG3350, 100 mM KCl	Resolution 2.20 Å R-free 0.215

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PGFRA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–151； UniProt 550–696 Author chain A； PDBConstruct 152–356； UniProt 769–973

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	6joj
Deposition date deposition_date	2019-03-22
Structure title title	Crystal structure of PDGFRA T674I in complex with crenolanib by soaking
Keywords keywords	PDGFRA, Inhibitor, crenolanib, ONCOPROTEIN; ONCOPROTEIN
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	20.89 Å
Radius of gyration Rg (electron density) rg_electron	19.76 Å
Forward intensity I(0) i0	25363900.00
Molecular weight molecular_weight	39230.0 kDa
Excluded volume excluded_volume	49340 Å³
Envelope volume envelope_volume	56978 Å³
Hydration-shell volume shell_volume	23427 Å³
Envelope diameter envelope_diameter	63.5 Å
Shell Rg shell_rg	26.77 Å
Envelope Rg envelope_rg	19.95 Å
Shape Rg shape_rg	19.73 Å
Total Rg total_rg	20.75 Å
Total atoms total_atoms	2750
Residues n_residues	338
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	70.5 Å
Rg (real space) rg_real	20.74 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	2.5360e+07
I(0) uncertainty (real space) i0_real_error	3.6140e+05
Rg (reciprocal space) rg_reciprocal	20.77 Å
I(0) (reciprocal space) i0_reciprocal	25360000.0000
Solution quality estimate total_estimate	0.7919
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.479
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7640000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; 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	Platelet-derived growth factor receptor alpha
Molecular weight formula_weight	40588.7 kDa
EC 编号 ec_number	2.7.10.1
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	2785

GAMDKQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGPIYIITEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSFTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine
Molecular weight formula_weight	443.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6joja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id	6jojA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	6jojA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	100.556 Å
Unit-cell length b length_b	100.556 Å
Unit-cell length c length_c	110.987 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	46.799 Å
R factor r_factor	0.2241
R_work r_work	0.2235
R_free r_free	0.2334

fit	/app/data/saxs_computation/jo/6joj/6joj.fit
pddf	/app/data/pr_computation/jo/6joj/6joj.pr.out
profile	/app/data/saxs_computation/jo/6joj/6joj.dat

Crystal structure of PDGFRA T674I in complex with crenolanib by soaking

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

Platelet-derived growth factor receptor alpha

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