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6gzd

Crystal structure of Human CSNK1A1 with A86

Method: X-RAY DIFFRACTION Dmax: 73.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Casein kinase I isoform alpha

Homo sapiens

UniProt P48729

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 1–337 Not recorded DMS DIMETHYL SULFOXIDE × 2 PGE TRIETHYLENE GLYCOL × 3 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 6 TCE 3,3',3''-phosphanetriyltripropanoic acid × 1 LCI [4-[[4-[5-(cyclopropylmethyl)-1-methyl-pyrazol-4-yl]-5-fluoranyl-pyrimidin-2-yl]amino]cyclohexyl]azanium × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days. Resolution 2.28 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 6GZD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–337（337 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–337（337 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
7WTT Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) Deposited 2022-02-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain a 1–337（337 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G66 Structure with SJ3149 Deposited 2023-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–337（337 aa）
Not recorded ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8G66 Structure with SJ3149 Deposited 2023-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–337（337 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
9OTY DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 10–303（294 aa）
Not recorded ZN ZINC ION × 1 A1CEH N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KC1A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 38–374； UniProt 1–337

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 6gzd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gzd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6gzd
Deposition date deposition_date2018-07-03
Structure title titleCrystal structure of Human CSNK1A1 with A86
Keywords keywordsCKIa, Casein kinase, Kinase inhibitor, Transferase; 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_guinier21.15 Å
Radius of gyration Rg (electron density) rg_electron20.02 Å
Forward intensity I(0) i022552600.00
Molecular weight molecular_weight37016.0 kDa
Excluded volume excluded_volume46783 ų
Envelope volume envelope_volume55338 ų
Hydration-shell volume shell_volume22648 ų
Envelope diameter envelope_diameter66.8 Å
Shell Rg shell_rg26.99 Å
Envelope Rg envelope_rg20.39 Å
Shape Rg shape_rg19.98 Å
Total Rg total_rg21.09 Å
Total atoms total_atoms2597
Residues n_residues297
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 dmax73.7 Å
Rg (real space) rg_real21.02 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real2.2550e+07
I(0) uncertainty (real space) i0_real_error3.2140e+05
Rg (reciprocal space) rg_reciprocal21.04 Å
I(0) (reciprocal space) i0_reciprocal22550000.0000
Solution quality estimate total_estimate0.7875
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary27.1 Å
Skewness Skewness skewness0.157
Kurtosis Kurtosis kurtosis-0.473
Angular range angular_range— – 0.3750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7268000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6gzda_
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.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id6gzdA01
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_id6gzdA02
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)