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Crystal structure of phosphorylated PT220 casein kinase I delta (CK1D), conformation 1
Analyse Crystal structure of phosphorylated PT220 casein kinase I delta (CK1D)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P7F
- Type
- protein
- Length
- 1,154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase I isoform delta
- EC
- 2.7.11.1, 2.7.11.26
- UniProt
- P48730
- Ligands
- AMP, ADN, SO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 292 | 39% helix, 18% strand | P48730 |
| C, D | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 285 | 40% helix, 19% strand | P48730 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ADN · Adenosine · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.83 | 0.96 | 43 | EDO |
| 2 | 323 | 0.75 | 0.86 | 60 | empty |
| 3 | 200 | 0.60 | 0.82 | 32 | AMP |
| 4 | 512 | 0.60 | 0.74 | 52 | SO4 |
| 5 | 484 | 0.59 | 0.74 | 57 | SO4 |
Interfaces
4 interfaces between chains.
- A–D · 655 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 646 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 363 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 7P7F · Crystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 1 · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 7P7F · PDBe 7P7F · UniProt P48730
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