Research workbench
Crystal structure of CDK5:P25 in complex with an ATP analogue
Analyse Crystal structure of CDK5:P25 in complex with an ATP analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O0G
- Type
- protein
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 5; Cyclin-dependent kinase 5 activator 1
- EC
- 2.7.11.22
- UniProt
- Q00535, Q15078
- Ligands
- 3O0
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 5 (EC 2.7.11.22) | protein | 289 | 34% helix, 18% strand | Q00535 |
| D, E | Cyclin-dependent kinase 5 activator 1 | protein | 149 | 70% helix, 0% strand | Q15078 |
| B | Cell division protein kinase 5 (EC 2.7.11.22) | protein | 264 | 38% helix, 14% strand | Q00535 |
Ligands and binding sites
- 3O0 · {4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.64 | 0.84 | 24 | empty |
| 2 | 189 | 0.59 | 0.81 | 22 | 3O0 |
| 3 | 113 | 0.52 | 0.82 | 23 | empty |
| 4 | 67 | 0.49 | 0.84 | 18 | empty |
| 5 | 106 | 0.47 | 0.79 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–D · 1459 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 1332 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3O0G · Crystal Structure of Cdk5:p25 in complex with an ATP analogue · 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 B 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 3O0G · PDBe 3O0G · UniProt Q00535 · UniProt Q15078
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