MolNFT v1 · #32913 · protein
Structure of CDK2-cyclin a with pha-533514
2C4G · Cell division protein kinase 2: “Structure of CDK2-cyclin a with pha-533514”. X-ray diffraction, 2 ligands (514, SO4), 18 pockets (best druggability 0.81). MolNFT v1 #32913 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2C4G
- Type
- protein
- Length
- 1,117 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
- 514, SO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 301 | 34% helix, 18% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 64% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 300 | 34% helix, 18% strand | P24941 |
Ligands and binding sites
- 514 · (3Z)-5-acetyl-3-(benzoylimino)-3,6-dihydropyrrolo[3,4-c]pyrazol-5-ium · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.81 | 0.97 | 22 | empty |
| 2 | 150 | 0.81 | 0.97 | 24 | empty |
| 3 | 473 | 0.68 | 0.79 | 39 | empty |
| 4 | 577 | 0.66 | 0.76 | 59 | empty |
| 5 | 552 | 0.66 | 0.77 | 60 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1568 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1528 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 455 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2C4G · Structure of CDK2-cyclin a with pha-533514 · 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 0.91
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 2C4G · PDBe 2C4G · UniProt P24941 · UniProt P20248
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