MolNFT v1 · #160025 · protein
Crystal structure of CDK4 in complex with CYCLIND1 and P27
6P8F · G1/S-specific cyclin-D1: “Crystal structure of CDK4 in complex with CYCLIND1 and P27”. X-ray diffraction, 10 pockets (best druggability 0.74). MolNFT v1 #160025 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P8F
- Type
- protein
- Length
- 562 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
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G1/S-specific cyclin-D1 | protein | 244 | 66% helix, 0% strand | P24385 |
| B | Cyclin-dependent kinase 4 (EC 2.7.11.22) | protein | 262 | 35% helix, 14% strand | P11802 |
| C | Cyclin-dependent kinase inhibitor 1B | protein | 56 | 41% helix, 11% strand | P46527 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.74 | 0.93 | 28 | empty |
| 2 | 61 | 0.57 | 0.89 | 14 | empty |
| 3 | 115 | 0.52 | 0.81 | 24 | empty |
| 4 | 280 | 0.51 | 0.74 | 37 | empty |
| 5 | 93 | 0.47 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1184 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1111 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 978 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6P8F · 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 0.94
- 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 0.87
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 6P8F · PDBe 6P8F · UniProt P24385 · UniProt P11802 · UniProt P46527
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