Research workbench
Crystal structure of casein kinase I delta (CK1D) in complex with double phosphorylated P63 PAD2P peptide
Analyse Crystal structure of casein kinase I delta (CK1D) in complex with double… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RU7
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- 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
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 4 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 | 292 | 39% helix, 18% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 288 | 40% helix, 19% strand | P48730 |
| C | Tumor protein 63 | protein | 15 | 27% helix, 7% strand | Q9H3D4 |
| D | Tumor protein 63 | protein | 13 | 23% helix, 8% strand | Q9H3D4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.76 | 0.85 | 67 | EDO |
| 2 | 256 | 0.65 | 0.83 | 38 | ADP, EDO |
| 3 | 216 | 0.61 | 0.81 | 28 | ADP |
| 4 | 206 | 0.46 | 0.74 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–C · 779 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 687 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 658 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6RU7 · Crystal structure of Casein Kinase I delta (CK1d) in complex with double phosphorylated… · 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 D against A, TM-score 0.44
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 6RU7 · PDBe 6RU7 · UniProt P48730 · UniProt Q9H3D4
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