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4crs

Human Protein Kinase N2 (PKN2, PRKCL2) in complex with ATPgammaS

Method: X-RAY DIFFRACTION Dmax: 69.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE/THREONINE-PROTEIN KINASE N2

HOMO SAPIENS

UniProt Q16513

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 646–984 Fragment：KINASE DOMAIN, RESIDUES 646-984 Non-standard monomer：Yes (specific site not provided by mmCIF) AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.8；2.3M AMMONIUM SULPHATE, 0.1M CITRATE PH 5.8, 0.2M SODIUM/POTASSIUM TARTRATE Resolution 2.75 Å R-free 0.262

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 4CRS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4RRV Crystal structure of PDK1 in complex with ATP and PIFtide Deposited 2014-11-06 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 969–983（15 aa） Fragment：PIFtide (PRK2 hydrophobic motif, UNP residues 969-983)
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21 mg/mL protein in 25 mM Tris, pH 7.5, 0.5 M sodium chloride, 1 mM DTT, 15 mM EDTA, 15 mM ATP, precipitant: 0.1 M HEPES, pH 7.5, 1.2 M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 1.41 Å R-free 0.163
6CCY Crystal structure of Akt1 in complex with a selective inhibitor Deposited 2018-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 969–983（15 aa）
Mutation：N199S, S396P, E397S, T433V Non-standard monomer：Yes (specific site not provided by mmCIF) EX4 (5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；16% PEG 3350 and 200mM Ammonium Formate
Resolution 2.18 Å R-free 0.276
6GBE Murine Protein Tyrosine Phosphatase PTPN13 PDZ3 Domain-PRK2 Peptide Complex Deposited 2018-04-13 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 973–984（12 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) PBS；Pressure 1
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-99% 15N] PDZ3/PRK2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PKN2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–341； UniProt 646–984

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4crs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4crs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4crs
Deposition date deposition_date2014-02-28
Structure title titleHuman Protein Kinase N2 (PKN2, PRKCL2) in complex with ATPgammaS
Keywords keywordsTRANSFERASE, PRKCL2, PKN2, AGC; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.51 Å
Radius of gyration Rg (electron density) rg_electron20.24 Å
Forward intensity I(0) i027132000.00
Molecular weight molecular_weight39071.0 kDa
Excluded volume excluded_volume48502 ų
Envelope volume envelope_volume57598 ų
Hydration-shell volume shell_volume23202 ų
Envelope diameter envelope_diameter69.8 Å
Shell Rg shell_rg27.38 Å
Envelope Rg envelope_rg20.65 Å
Shape Rg shape_rg20.23 Å
Total Rg total_rg21.18 Å
Total atoms total_atoms2737
Residues n_residues331
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.4 Å
Rg (real space) rg_real21.40 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real2.7130e+07
I(0) uncertainty (real space) i0_real_error3.2060e+05
Rg (reciprocal space) rg_reciprocal21.42 Å
I(0) (reciprocal space) i0_reciprocal27130000.0000
Solution quality estimate total_estimate0.8897
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.5 Å
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.368
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7551000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4crsa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd4crsa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id4crsA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4crsA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)