MolNFT v1 · #163153 · protein
Crystal structure of casein kinase I delta (CK1D) in complex with triple phosphorylated P63 PAD3P peptide
6RU8 · Casein kinase I isoform delta: “Crystal structure of casein kinase I delta (CK1D) in complex with triple phosphorylated P63 PAD3P peptide”. X-ray diffraction, 3 ligands (ADP, NA, SO4), 12 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 6RU8
- Type
- protein
- Length
- 1,206 residues
- Chains
- 8
- 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
- ADP, NA, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 293 | 38% helix, 19% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 287 | 39% helix, 19% strand | P48730 |
| E | Tumor protein 63 | protein | 10 | 40% helix, 10% strand | Q9H3D4 |
| F | Tumor protein 63 | protein | 12 | 33% helix, 8% strand | Q9H3D4 |
| G, H | Tumor protein 63 | protein | 9 | 44% helix, 11% strand | Q9H3D4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, F, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.82 | 0.95 | 42 | EDO |
| 2 | 532 | 0.76 | 0.83 | 69 | EDO |
| 3 | 667 | 0.73 | 0.79 | 69 | empty |
| 4 | 96 | 0.72 | 0.95 | 25 | empty |
| 5 | 277 | 0.64 | 0.81 | 32 | empty |
Interfaces
13 interfaces between chains.
- B–F · 845 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 647 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 604 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 577 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 6RU8 · Crystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9H3D4 · AlphaFold monomer V2.0 prediction for tumor protein 63 (Q9H3D4) · a predicted model of the same protein · chain G against A, TM-score 0.43
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 6RU8 · PDBe 6RU8 · UniProt P48730 · UniProt Q9H3D4
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