SAXSdb — 4otd

▼

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 605–942	Fragment：UNP residues 605-942 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 4OTD	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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	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 mutation/modification 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, 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
4OTG Crystal Structure of PRK1 Catalytic Domain in Complex with Lestaurtinib Deposited 2014-02-13	Different ligand/ion 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 ligand/ion 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 ligand/ion 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
9RXE Solution structure of the HR1c domain of human PKN1 Deposited 2025-07-11	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 201–297（97 aa）	Not recorded	No recorded non-water small molecule	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

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 4–341； UniProt 605–942

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4otd
Deposition date deposition_date	2014-02-13
Structure title title	Crystal Structure of PRK1 Catalytic Domain
Keywords keywords	PRK1, PKN1, Protein kinase C related kinase 1, KINASE, Protein Kinase, ATP Binding, Phosphorylation, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.64 Å
Radius of gyration Rg (electron density) rg_electron	20.39 Å
Forward intensity I(0) i0	23809000.00
Molecular weight molecular_weight	37688.0 kDa
Excluded volume excluded_volume	47332 Å³
Envelope volume envelope_volume	56316 Å³
Hydration-shell volume shell_volume	22765 Å³
Envelope diameter envelope_diameter	71.7 Å
Shell Rg shell_rg	27.30 Å
Envelope Rg envelope_rg	20.63 Å
Shape Rg shape_rg	20.39 Å
Total Rg total_rg	21.33 Å
Total atoms total_atoms	2656
Residues n_residues	334
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

▼

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

Maximum dimension Dmax dmax	69.2 Å
Rg (real space) rg_real	21.52 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.3810e+07
I(0) uncertainty (real space) i0_real_error	2.8440e+05
Rg (reciprocal space) rg_reciprocal	21.54 Å
I(0) (reciprocal space) i0_reciprocal	23810000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.187
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7576000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.993

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4otda_
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.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4otdA01
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	4otdA02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	56.147 Å
Unit-cell length b length_b	72.628 Å
Unit-cell length c length_c	94.457 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	2.000 Å
Low-resolution limit resolution_low	36.130 Å
R factor r_factor	0.1770
R_work r_work	0.1747
R_free r_free	0.2214

Description description	Serine/threonine-protein kinase N1
Molecular weight formula_weight	38341.5 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	3027

Crystal Structure of PRK1 Catalytic Domain

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Trichoplusia ni

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

fit	/app/data/saxs_computation/ot/4otd/4otd.fit
pddf	/app/data/pr_computation/ot/4otd/4otd.pr.out
profile	/app/data/saxs_computation/ot/4otd/4otd.dat