Research workbench
Crystal structure of human casein kinase I delta in complex with iwp-2
Analyse Crystal structure of human casein kinase I delta in complex with iwp-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OKT
- Type
- protein
- Length
- 1,135 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
- 9XK, SO4
- Pockets
- 11 · best druggability 0.77
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 | 286 | 39% helix, 19% strand | P48730 |
| B | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 282 | 40% helix, 19% strand | P48730 |
| C | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 285 | 39% helix, 17% strand | P48730 |
| D | Casein kinase I isoform delta (EC 2.7.11.1, 2.7.11.26) | protein | 282 | 39% helix, 17% strand | P48730 |
Ligands and binding sites
- 9XK · ~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 19 copies · chains A, D, C, B
- GOL · Glycerol · additive · 4 copies · chains B, A, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.77 | 0.81 | 79 | SO4, ACT, GOL |
| 2 | 834 | 0.77 | 0.80 | 90 | SO4 |
| 3 | 180 | 0.64 | 0.84 | 29 | 9XK |
| 4 | 188 | 0.62 | 0.83 | 28 | 9XK |
| 5 | 200 | 0.62 | 0.82 | 28 | 9XK |
Interfaces
4 interfaces between chains.
- A–C · 602 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 594 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 380 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 378 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5OKT · Crystal structure of human Casein Kinase I delta in complex with IWP-2 · 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 5OKT · PDBe 5OKT · UniProt P48730
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