9y8k

Crystal structure of the Kelch domain of human KLHL12 with compound 7k

Method: X-RAY DIFFRACTION Dmax: 64.5 Å Quality: REASONABLE

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

Kelch-like protein 12

Homo sapiens

UniProt Q53G59

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 279–567 Not recorded A1CTR 2-(2-amino-4-methyl-1H-1,3-benzimidazol-1-yl)-N-(2,4,6-trichlorophenyl)acetamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;0.1M Bis-Tris pH 5.5, 0.2M MgCl2 and 25% PEG3350 Resolution 1.27 Å R-free 0.191

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.

16 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KLH12_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 7–295; UniProt 279–567

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 9y8k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y8k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y8k
Deposition date deposition_date2025-09-11
Structure title titleCrystal structure of the Kelch domain of human KLHL12 with compound 7k
Keywords keywordsE3 ligase, fragment-based drug discovery, PROTAC, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.47
Radius of gyration Rg (electron density) rg_electron17.51
Forward intensity I(0) i033225600.00
Molecular weight molecular_weight29295.0 kDa
Excluded volume excluded_volume28011 ų
Envelope volume envelope_volume43108 ų
Hydration-shell volume shell_volume19923 ų
Envelope diameter envelope_diameter56.6
Shell Rg shell_rg24.47
Envelope Rg envelope_rg17.64
Shape Rg shape_rg17.49
Total Rg total_rg18.23
Total atoms total_atoms2204
Residues n_residues287
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 dmax64.5
Rg (real space) rg_real18.32
Rg uncertainty (real space) rg_real_error0.41
I(0) (real space) i0_real3.3230e+07
I(0) uncertainty (real space) i0_real_error4.4550e+05
Rg (reciprocal space) rg_reciprocal18.34
I(0) (reciprocal space) i0_reciprocal33230000.0000
Solution quality estimate total_estimate0.5990
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.7
Skewness Skewness skewness0.034
Kurtosis Kurtosis kurtosis-0.537
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15040000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.669; Stabil: 1.000; Sysdev: 0.259; Positv: 1.000; Valcen: 1.000; 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)