Research workbench
Crystal structure of CDK4 in complex with CYCLIND1 and P27
Analyse Crystal structure of CDK4 in complex with CYCLIND1 and P27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P8E
- Type
- protein
- Length
- 564 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G1/S-specific cyclin-D1; Cyclin-dependent kinase 4; Cyclin-dependent kinase inhibitor 1B
- EC
- 2.7.11.22
- UniProt
- P24385, P11802, P46527
- Ligands
- MG
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G1/S-specific cyclin-D1 | protein | 247 | 70% helix, 0% strand | P24385 |
| B | Cyclin-dependent kinase 4 (EC 2.7.11.22) | protein | 260 | 40% helix, 15% strand | P11802 |
| C | Cyclin-dependent kinase inhibitor 1B | protein | 57 | 40% helix, 11% strand | P46527 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.58 | 0.81 | 34 | empty |
| 2 | 70 | 0.58 | 0.88 | 15 | empty |
| 3 | 343 | 0.55 | 0.74 | 31 | empty |
| 4 | 55 | 0.51 | 0.87 | 21 | empty |
| 5 | 117 | 0.48 | 0.79 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1170 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1067 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 984 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6P8E · Crystal structure of CDK4 in complex with CyclinD1 and P27 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.95
- 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 0.95
- P46527 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase inhibitor 1B (P46527) · a predicted model of the same protein · chain C against A, TM-score 0.84
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
- Every structure of UniProt P46527
- Elsewhere: RCSB PDB 6P8E · PDBe 6P8E · UniProt P24385 · UniProt P11802 · UniProt P46527
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.