Research workbench
Crystal structure of casein kinase I delta (CK1D) in complex with monophosphorylated P63 PAD1P peptide
Analyse Crystal structure of casein kinase I delta (CK1D) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RU6
- Type
- protein
- Length
- 574 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase I isoform delta; Tumor protein 63
- EC
- 2.7.11.1, 2.7.11.26
- UniProt
- P48730, Q9H3D4
- Ligands
- ACP, NA, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 288 | 38% helix, 18% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 278 | 41% helix, 18% strand | P48730 |
| C | Tumor protein 63 | protein | 8 | 0% helix, 0% strand | Q9H3D4 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.82 | 0.96 | 41 | empty |
| 2 | 235 | 0.55 | 0.77 | 32 | ACP |
| 3 | 119 | 0.45 | 0.78 | 22 | ACP |
| 4 | 102 | 0.44 | 0.79 | 23 | empty |
| 5 | 155 | 0.40 | 0.73 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 648 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 460 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6RU6 · Crystal structure of Casein Kinase I delta (CK1d) in complex with monophosphorylated p63… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3D4 · AlphaFold monomer V2.0 prediction for tumor protein 63 (Q9H3D4) · a predicted model of the same protein · chain C against A, TM-score 0.70
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P48730
- Every structure of UniProt Q9H3D4
- Elsewhere: RCSB PDB 6RU6 · PDBe 6RU6 · UniProt P48730 · UniProt Q9H3D4
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