MolNFT v1 · #25907 · protein
The structural basis of CDK2 activation by cyclin E
1W98 · Cell division protein kinase 2: “The structural basis of CDK2 activation by cyclin E”. X-ray diffraction, 4 pockets (best druggability 0.80). MolNFT v1 #25907 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1W98
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; G1/S-specific cyclin E1
- EC
- 2.7.1.37
- UniProt
- P24941, P24864
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 298 | 35% helix, 18% strand | P24941 |
| B | G1/S-specific cyclin E1 | protein | 270 | 63% helix, 1% strand | P24864 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.80 | 0.92 | 49 | empty |
| 2 | 477 | 0.68 | 0.79 | 54 | empty |
| 3 | 160 | 0.56 | 0.81 | 34 | empty |
| 4 | 119 | 0.41 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1897 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1W98 · The structural basis of CDK2 activation by cyclin E · the same entry in another collection · chain A against A, TM-score 1.00
- P24864 · AlphaFold monomer V2.0 prediction for G1/S-specific cyclin-E1 (P24864) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P24941
- Every structure of UniProt P24864
- Elsewhere: RCSB PDB 1W98 · PDBe 1W98 · UniProt P24941 · UniProt P24864
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