MolNFT v1 · #143227 · protein
CDK2/CYCLIN A/P27-kid-deltac
6ATH · Cyclin-dependent kinase 2: “CDK2/CYCLIN A/P27-kid-deltac”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.80). MolNFT v1 #143227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ATH
- Type
- protein
- Length
- 588 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2; Cyclin-dependent kinase inhibitor 1B
- EC
- 2.7.11.22
- UniProt
- P24941, P20248, P46527
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 278 | 36% helix, 14% strand | P24941 |
| B | Cyclin-A2 | protein | 260 | 68% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase inhibitor 1B | protein | 50 | 32% helix, 18% strand | P46527 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.80 | 0.98 | 22 | empty |
| 2 | 300 | 0.63 | 0.80 | 37 | empty |
| 3 | 137 | 0.55 | 0.82 | 29 | empty |
| 4 | 191 | 0.52 | 0.77 | 26 | empty |
| 5 | 204 | 0.51 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1767 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1037 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 971 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6ATH · Cdk2/cyclin A/p27-KID-deltaC · the same entry in another collection · chain A against A, 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 0.90
- P46527 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase inhibitor 1B (P46527) · a predicted model of the same protein · chain C against A, TM-score 0.66
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
- Every structure of UniProt P46527
- Elsewhere: RCSB PDB 6ATH · PDBe 6ATH · UniProt P24941 · UniProt P20248 · UniProt P46527
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