MolNFT v1 · #80137 · protein
Structure of CDK2/CYCLIN a in complex with CAN508
3TNW · Cyclin-dependent kinase 2: “Structure of CDK2/CYCLIN a in complex with CAN508”. X-ray diffraction, 2 ligands (F18, NA), 12 pockets (best druggability 0.80). MolNFT v1 #80137 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3TNW
- Type
- protein
- Length
- 1,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P30274
- Ligands
- F18, NA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 296 | 35% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 66% helix, 0% strand | P30274 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 292 | 35% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 69% helix, 0% strand | P30274 |
Ligands and binding sites
- F18 · 4-[(E)-(3,5-diamino-1H-pyrazol-4-yl)diazenyl]phenol · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.80 | 0.98 | 25 | empty |
| 2 | 117 | 0.80 | 0.98 | 23 | empty |
| 3 | 1121 | 0.73 | 0.76 | 98 | empty |
| 4 | 319 | 0.68 | 0.82 | 34 | F18 |
| 5 | 266 | 0.67 | 0.83 | 35 | F18 |
Interfaces
5 interfaces between chains.
- C–D · 1709 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1655 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 486 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 464 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3TNW · Structure of CDK2/cyclin A in complex with CAN508 · the same entry in another collection · chain D against D, TM-score 1.00
- P30274 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P30274) · 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 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 P30274
- Elsewhere: RCSB PDB 3TNW · PDBe 3TNW · UniProt P24941 · UniProt P30274
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