Research workbench
Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin
Analyse Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XO2
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens; Saimiriine herpesvirus 2
- Molecule
- Cyclin; Cell division protein kinase 6
- EC
- 2.7.1.37
- UniProt
- Q01043, Q00534
- Ligands
- FSE
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.9 · 2 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin | protein | 243 | 61% helix, 1% strand | Q01043 |
| B | Cell division protein kinase 6 (EC 2.7.1.37) | protein | 289 | 32% helix, 19% strand | Q00534 |
Ligands and binding sites
- FSE · 3,7,3',4'-tetrahydroxyflavone · 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 | 497 | 0.75 | 0.83 | 39 | empty |
| 2 | 249 | 0.68 | 0.84 | 37 | FSE |
| 3 | 101 | 0.54 | 0.84 | 21 | empty |
| 4 | 154 | 0.47 | 0.77 | 30 | empty |
| 5 | 76 | 0.41 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2190 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1XO2 · Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00534 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 6 (Q00534) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q01043
- Every structure of UniProt Q00534
- Elsewhere: RCSB PDB 1XO2 · PDBe 1XO2 · UniProt Q01043 · UniProt Q00534
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