9y8v

Crystal structure of the Kelch domain of human KLHL12 with compound 10q

Method: X-RAY DIFFRACTION Dmax: 55.4 Å Quality: EXCELLENT

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 A1CTF 2-{4-[(1R,2S)-2-{[(3S)-3-(1,1-dioxo-1lambda~6~-thiomorpholin-4-yl)pyrrolidin-1-yl]methyl}cyclopropyl]-2-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 0.199

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 9y8v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9y8v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9y8v
Deposition date deposition_date2025-09-11
Structure title titleCrystal structure of the Kelch domain of human KLHL12 with compound 10q
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_guinier18.60
Radius of gyration Rg (electron density) rg_electron17.37
Forward intensity I(0) i017618100.00
Molecular weight molecular_weight31355.0 kDa
Excluded volume excluded_volume38926 ų
Envelope volume envelope_volume42322 ų
Hydration-shell volume shell_volume19666 ų
Envelope diameter envelope_diameter56.4
Shell Rg shell_rg24.44
Envelope Rg envelope_rg17.57
Shape Rg shape_rg17.32
Total Rg total_rg18.45
Total atoms total_atoms4314
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 dmax55.4
Rg (real space) rg_real18.44
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real1.7620e+07
I(0) uncertainty (real space) i0_real_error2.1360e+05
Rg (reciprocal space) rg_reciprocal18.47
I(0) (reciprocal space) i0_reciprocal17620000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.0
Skewness Skewness skewness0.021
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.4300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7341000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)