Research workbench
Crystal structure of CLK1 in complex with 5-iodotubercidin
Analyse Crystal structure of CLK1 in complex with 5-iodotubercidin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G33
- Type
- protein
- Length
- 1,011 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein kinase CLK1
- EC
- 2.7.12.1
- UniProt
- P49759
- Ligands
- 5ID, IOD, PO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 337 | 39% helix, 21% strand | P49759 |
Ligands and binding sites
- 5ID · (2R,3R,4S,5R)-2-(4-amino-5-iodo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3, 4-diol · ligand · 3 copies · chains A, B, C
- IOD · Iodide ion · ion · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.82 | 0.83 | 105 | 5ID, IOD |
| 2 | 1018 | 0.74 | 0.77 | 71 | empty |
| 3 | 380 | 0.72 | 0.83 | 54 | 5ID, IOD |
| 4 | 324 | 0.68 | 0.82 | 45 | 5ID, IOD |
| 5 | 215 | 0.61 | 0.81 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1029 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 444 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 185 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6G33 · Crystal structure of CLK1 in complex with 5-iodotubercidin · the same entry in another collection · chain A against A, TM-score 1.00
- P49759 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK1 (P49759) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P49759
- Elsewhere: RCSB PDB 6G33 · PDBe 6G33 · UniProt P49759
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