MolNFT v1 · #18299 · protein
The crystal structure of ucn-01 in complex with phospho-CDK2/CYCLIN a
1PKD · Cell division protein kinase 2: “The crystal structure of ucn-01 in complex with phospho-CDK2/CYCLIN a”. X-ray diffraction, 1 ligand (UCN), 12 pockets (best druggability 0.80). MolNFT v1 #18299 on GenesisL1: 3D structure, binding…
- PDB
- 1PKD
- Type
- protein
- Length
- 1,110 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2
- EC
- 2.7.1.-
- UniProt
- P24941, P20248
- Ligands
- UCN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.-) | protein | 297 | 34% helix, 18% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 66% helix, 0% strand | P20248 |
Ligands and binding sites
- UCN · 7-hydroxystaurosporine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.80 | 0.99 | 23 | empty |
| 2 | 115 | 0.79 | 0.98 | 23 | empty |
| 3 | 346 | 0.66 | 0.80 | 36 | UCN |
| 4 | 299 | 0.65 | 0.81 | 37 | UCN |
| 5 | 272 | 0.61 | 0.80 | 40 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1805 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1756 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1PKD · The crystal structure of ucn-01 in complex with phospho-CDK2/CYCLIN a · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · 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 0.91
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 P20248
- Elsewhere: RCSB PDB 1PKD · PDBe 1PKD · UniProt P24941 · UniProt P20248
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