8ws1

Crystal structure of human NEK7 D161N mutant

Method: X-RAY DIFFRACTION Dmax: 88.4 Å Quality: GOOD

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

Serine/threonine-protein kinase Nek7

Homo sapiens

UniProt Q8TDX7

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–302 Chain B; UniProt 1–302 Mutation:D161N EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;294 K;0.1 M Tris pH 8.4, PEG 8000 15% Resolution 2.40 Å R-free 0.238

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.

12 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEK7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–302; UniProt 1–302 Author chain B; PDBConstruct 1–302; UniProt 1–302

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 8ws1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ws1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ws1
Deposition date deposition_date2023-10-16
最后修订 last_revision2025-04-16
Structure title titleCrystal structure of human NEK7 D161N mutant
Keywords keywordsKinase, Complex, autoinhibitory, human, inflammasomes, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.75
Radius of gyration Rg (electron density) rg_electron25.70
Forward intensity I(0) i062085800.00
Molecular weight molecular_weight62237.0 kDa
Excluded volume excluded_volume78342 ų
Envelope volume envelope_volume96299 ų
Hydration-shell volume shell_volume31050 ų
Envelope diameter envelope_diameter95.9
Shell Rg shell_rg33.10
Envelope Rg envelope_rg25.82
Shape Rg shape_rg25.68
Total Rg total_rg26.55
Total atoms total_atoms4367
Residues n_residues538
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax88.4
Rg (real space) rg_real26.69
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real6.2090e+07
I(0) uncertainty (real space) i0_real_error9.4610e+05
Rg (reciprocal space) rg_reciprocal26.71
I(0) (reciprocal space) i0_reciprocal62090000.0000
Solution quality estimate total_estimate0.8097
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary31.4
Skewness Skewness skewness0.306
Kurtosis Kurtosis kurtosis-0.309
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12830000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.845; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)