Research workbench
Structural mechanism for the inhibition of CD5-P25 from the roscovitine, aloisine and indirubin.
Analyse Structural mechanism for the inhibition of CD5-P25 from the roscovitine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UNL
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 5; Cyclin-dependent kinase 5 activator 1
- EC
- 2.7.1.-
- UniProt
- Q00535, Q15078
- Ligands
- RRC
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclin-dependent kinase 5 (EC 2.7.1.-) | protein | 292 | 34% helix, 17% strand | Q00535 |
| D, E | Cyclin-dependent kinase 5 activator 1 | protein | 149 | 69% helix, 0% strand | Q15078 |
Ligands and binding sites
- RRC · R-roscovitine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.65 | 0.83 | 35 | empty |
| 2 | 198 | 0.63 | 0.83 | 25 | RRC |
| 3 | 106 | 0.55 | 0.84 | 23 | empty |
| 4 | 124 | 0.55 | 0.83 | 23 | empty |
| 5 | 110 | 0.46 | 0.79 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1496 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1495 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1UNL · Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and… · the same entry in another collection · chain E against E, TM-score 1.00
- Q15078 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 5 activator 1 (Q15078) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q00535 · AlphaFold monomer V2.0 prediction for cyclin-dependent-like kinase 5 (Q00535) · a predicted model of the same protein · chain A 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 Q00535
- Every structure of UniProt Q15078
- Elsewhere: RCSB PDB 1UNL · PDBe 1UNL · UniProt Q00535 · UniProt Q15078
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