SAXSdb — 9rxe

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

Serine/threonine-protein kinase N1

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 201–297	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.3；298 K；Ionic strength (raw mmCIF value) 0.17；Pressure 1 NMR measurement conditions：pH 7.3；298 K；Ionic strength (raw mmCIF value) 0.17；Pressure 1 NMR sample composition：1.6 mM [U-100% 15N] PRK1 HR1c domain, 150 mM sodium chloride, 20 mM sodium phosphate, 90 % H2O, 10 % [U-2H] D2O, 0.05 % w/v sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1.2 mM [U-100% 13C; U-100% 15N] PRK1 HR1c domain, 150 mM sodium chloride, 20 mM sodium phosphate, 90 % H2O, 10 % [U-2H] D2O, 0.05 % w/v sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 9RXE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CXZ CRYSTAL STRUCTURE OF HUMAN RHOA COMPLEXED WITH THE EFFECTOR DOMAIN OF THE PROTEIN KINASE PKN/PRK1 Deposited 1999-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 13–98（86 aa） Fragment：RESIDUES 13 - 98	Not recorded	MG MAGNESIUM ION × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；277 K；PEG 300, pH 6.5, MICROBATCH, temperature 277K	Resolution 2.20 Å R-free 0.268
1URF HR1b domain from PRK1 Deposited 2003-10-29	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 122–199（78 aa） Fragment：HR1B, RESIDUES 122-199	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 60；Pressure 1	Resolution not provided
2RMK Rac1/PRK1 Complex Deposited 2007-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 122–199（78 aa） Fragment：HR1b domain, REM 2, UNP residues 122-199	Not recorded	MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0.225；Pressure ambient NMR sample composition 0.6mM [U-13C; U-15N; U-2H] Rac1; 0.6mM PRK1 HR1b; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6mM [U-100% 13C; U-100% 15N] Rac1; 0.6mM PRK1 HR1b; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6mM [U-100% 15N] Rac1; 0.6mM PRK1 HR1b; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6mM [U-100% 13C; U-100% 15N] Rac1; 0.6mM PRK1 Rac1; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6mM [U-100% 15N] HR1b; 0.6mM PRK1 Rac1; 0.7mM PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
4NKG Crystal structure of SspH1 LRR domain in complex PKN1 HR1b domain Deposited 2013-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 122–199（78 aa） Fragment：HR1b domain, REM 2 domain, UNP residues 122-199	Not recorded	HEZ HEXANE-1,6-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；26% PEG3350, 0.18M tri-Ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.242
4NKG Crystal structure of SspH1 LRR domain in complex PKN1 HR1b domain Deposited 2013-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 122–199（78 aa） Fragment：HR1b domain, REM 2 domain, UNP residues 122-199	Not recorded	HEZ HEXANE-1,6-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293 K；26% PEG3350, 0.18M tri-Ammonium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.242
4OTD Crystal Structure of PRK1 Catalytic Domain Deposited 2014-02-13	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 605–942（338 aa） Fragment：UNP residues 605-942	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；100mM Tris pH 8.5, 150-225mM Ammonium acetate, 23-28% PEG 3350, Vapor diffusion	Resolution 2.00 Å R-free 0.221
4OTG Crystal Structure of PRK1 Catalytic Domain in Complex with Lestaurtinib Deposited 2014-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 605–942（338 aa） Fragment：UNP residues 605-942	Non-standard monomer：Yes (specific site not provided by mmCIF)	2V9 Lestaurtinib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；100mM Tris pH 8.5, 150-225mM Ammonium acetate, 23-28% PEG 3350, Vapor diffusion	Resolution 2.60 Å R-free 0.268
4OTH Crystal Structure of PRK1 Catalytic Domain in Complex with Ro-31-8220 Deposited 2014-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 605–942（338 aa） Fragment：UNP residues 605-942	Non-standard monomer：Yes (specific site not provided by mmCIF)	DRN BISINDOLYLMALEIMIDE IX × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；100mM Tris pH 8.5, 150-225mM Ammonium acetate, 23-28% PEG 3350, Vapor diffusion	Resolution 1.80 Å R-free 0.266
4OTI Crystal Structure of PRK1 Catalytic Domain in Complex with Tofacitinib Deposited 2014-02-13	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 605–942（338 aa） Fragment：UNP residues 605-942	Non-standard monomer：Yes (specific site not provided by mmCIF)	MI1 3-{(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}-3-oxopropanenitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；100mM Tris pH 8.5, 150-225mM Ammonium acetate, 23-28% PEG 3350, Vapor diffusion	Resolution 1.93 Å R-free 0.226

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–104； UniProt 201–297

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	9rxe
Deposition date deposition_date	2025-07-11
最后修订 last_revision	2025-12-31
Structure title title	Solution structure of the HR1c domain of human PKN1
Keywords keywords	PKN1, HR1c, PRK1, COILED COIL, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.99 Å
Radius of gyration Rg (electron density) rg_electron	18.32 Å
Forward intensity I(0) i0	3937370000.00
Molecular weight molecular_weight	510520.0 kDa
Excluded volume excluded_volume	631750 Å³
Envelope volume envelope_volume	61072 Å³
Hydration-shell volume shell_volume	20681 Å³
Envelope diameter envelope_diameter	91.9 Å
Shell Rg shell_rg	32.02 Å
Envelope Rg envelope_rg	27.15 Å
Shape Rg shape_rg	18.28 Å
Total Rg total_rg	18.64 Å
Total atoms total_atoms	72765
Residues n_residues	4680
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	48.5 Å
Rg (real space) rg_real	16.65 Å
Rg uncertainty (real space) rg_real_error	0.09 Å
I(0) (real space) i0_real	3.7390e+09
I(0) uncertainty (real space) i0_real_error	3.5820e+07
Rg (reciprocal space) rg_reciprocal	18.39 Å
I(0) (reciprocal space) i0_reciprocal	3937000000.0000
Solution quality estimate total_estimate	0.6656
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	16.4 Å
Skewness Skewness skewness	0.436
Kurtosis Kurtosis kurtosis	-0.502
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	3.7750
Highest regularization parameter α highest_alpha	238300.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.009; Oscil: 0.921; Stabil: 0.986; Sysdev: 0.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (2)

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Description description	Serine/threonine-protein kinase N1
Molecular weight formula_weight	11366.9 kDa
EC 编号 ec_number	2.7.11.13
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	72765

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 BL21(DE3)

fit	/app/data/saxs_computation/rx/9rxe/9rxe.fit
pddf	/app/data/pr_computation/rx/9rxe/9rxe.pr.out
profile	/app/data/saxs_computation/rx/9rxe/9rxe.dat

Solution structure of the HR1c domain of human PKN1

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

Serine/threonine-protein kinase N1

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)