MolNFT v1 · #33410 · protein
Mechanism of cdk inhibition by active site phosphorylation: CDK2 Y15P T160P in complex with cyclin a structure
2CJM · Cell division protein kinase 2: “Mechanism of cdk inhibition by active site phosphorylation: CDK2 Y15P T160P in complex with cyclin a structure”. X-ray diffraction, 2 ligands (ATP, MG), 13 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 2CJM
- Type
- protein
- Length
- 1,097 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- ATP, MG
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 287 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin A2 | protein | 257 | 67% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 34% helix, 18% strand | P24941 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.81 | 0.99 | 23 | empty |
| 2 | 124 | 0.81 | 0.99 | 23 | empty |
| 3 | 861 | 0.74 | 0.78 | 91 | empty |
| 4 | 484 | 0.69 | 0.80 | 54 | ATP, MG |
| 5 | 479 | 0.68 | 0.79 | 53 | ATP |
Interfaces
5 interfaces between chains.
- C–D · 1722 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1628 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 487 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 2CJM · Mechanism of CDK inhibition by active site phosphorylation: CDK2 Y15p T160p in complex… · 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 D 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 2CJM · PDBe 2CJM · UniProt P24941 · UniProt P20248
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