Research workbench
Structure of phosphorylated THR160 CDK2/CYCLIN a in complex with the inhibitor variolin B
Analyse Structure of phosphorylated THR160 CDK2/CYCLIN a in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BHV
- Type
- protein
- Length
- 1,094 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P30274
- Ligands
- VAR, MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 298 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 262 | 68% helix, 0% strand | P30274 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 272 | 35% helix, 19% strand | P24941 |
Ligands and binding sites
- VAR · 9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SGM · Monothioglycerol · additive · 3 copies · chains A, B, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.81 | 0.99 | 24 | empty |
| 2 | 110 | 0.81 | 0.99 | 21 | empty |
| 3 | 927 | 0.75 | 0.78 | 88 | empty |
| 4 | 349 | 0.71 | 0.83 | 37 | VAR |
| 5 | 237 | 0.67 | 0.84 | 26 | VAR |
Interfaces
5 interfaces between chains.
- C–D · 1942 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1904 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 506 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 478 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 3BHV · Structure of phosphorylated Thr160 CDK2/cyclin A in complex with the inhibitor variolin B · 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 B 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 0.91
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 P30274
- Elsewhere: RCSB PDB 3BHV · PDBe 3BHV · UniProt P24941 · UniProt P30274
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