Research workbench
Crystal structure of CDK4 in complex with a D-type cyclin
Analyse Crystal structure of CDK4 in complex with a D-type cyclin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W96
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G1/S-specific cyclin-D1; Cell division protein kinase 4
- EC
- 2.7.11.22
- UniProt
- P24385, P11802
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G1/S-specific cyclin-D1 | protein | 249 | 65% helix, 0% strand | P24385 |
| B | Cell division protein kinase 4 (EC 2.7.11.22) | protein | 267 | 35% helix, 19% strand | P11802 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.66 | 0.84 | 28 | empty |
| 2 | 206 | 0.51 | 0.76 | 19 | empty |
| 3 | 173 | 0.47 | 0.76 | 22 | empty |
| 4 | 128 | 0.46 | 0.78 | 21 | empty |
| 5 | 57 | 0.43 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2W96 · Crystal Structure of CDK4 in complex with a D-type cyclin · the same entry in another collection · chain A against A, TM-score 1.00
- P11802 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 4 (P11802) · a predicted model of the same protein · chain B against A, TM-score 0.96
- P24385 · AlphaFold monomer V2.0 prediction for G1/S-specific cyclin-D1 (P24385) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P24385
- Every structure of UniProt P11802
- Elsewhere: RCSB PDB 2W96 · PDBe 2W96 · UniProt P24385 · UniProt P11802
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