MolNFT v1 · #11644 · protein
Phosphorylated cyclin-dependent kinase-2 bound to cyclin a
1JST: “Phosphorylated cyclin-dependent kinase-2 bound to cyclin a”. X-ray diffraction, 2 ligands (ATP, MN), 14 pockets (best druggability 0.81). MolNFT v1 #11644 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JST
- Type
- protein
- Length
- 1,112 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase-2; Cyclin a
- EC
- 2.7.1.-
- UniProt
- P24941, P20248
- Ligands
- ATP, MN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclin-dependent kinase-2 (EC 2.7.1.-) | protein | 298 | 34% helix, 15% strand | P24941 |
| B, D | Cyclin a | protein | 258 | 67% helix, 0% strand | P20248 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.81 | 0.98 | 25 | empty |
| 2 | 165 | 0.79 | 0.95 | 26 | empty |
| 3 | 710 | 0.72 | 0.78 | 71 | empty |
| 4 | 236 | 0.66 | 0.83 | 27 | MN, ATP |
| 5 | 349 | 0.65 | 0.80 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1729 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1667 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 461 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 445 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 127 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1JST · Phosphorylated cyclin-dependent kinase-2 bound to 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 C against A, TM-score 0.92
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 1JST · PDBe 1JST · UniProt P24941 · UniProt P20248
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