MolNFT v1 · #6632 · protein
Cyclin a-cyclin-dependent kinase 2 complex
1FIN: “Cyclin a-cyclin-dependent kinase 2 complex”. X-ray diffraction, 1 ligand (ATP), 14 pockets (best druggability 0.81). MolNFT v1 #6632 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FIN
- Type
- protein
- Length
- 1,116 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
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclin-dependent kinase 2 (EC 2.7.1.-) | protein | 298 | 35% helix, 18% strand | P24941 |
| B, D | Cyclin a | protein | 260 | 66% helix, 0% strand | P20248 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.81 | 0.98 | 23 | empty |
| 2 | 164 | 0.79 | 0.95 | 24 | empty |
| 3 | 883 | 0.76 | 0.79 | 86 | empty |
| 4 | 510 | 0.67 | 0.78 | 63 | empty |
| 5 | 311 | 0.65 | 0.81 | 36 | ATP |
Interfaces
5 interfaces between chains.
- C–D · 1780 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1764 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 442 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 404 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1FIN · Cyclin a-cyclin-dependent kinase 2 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 0.99
- 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 0.92
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 1FIN · PDBe 1FIN · UniProt P24941 · UniProt P20248
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