Research workbench
Crystal structure of CDK4 in complex with CyclinD1 and P21
Analyse Crystal structure of CDK4 in complex with CyclinD1 and P21 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P8H
- Type
- protein
- Length
- 556 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.19
- Source
- Homo sapiens
- Molecule
- G1/S-specific cyclin-D1; Cyclin-dependent kinase 4; Cyclin-dependent kinase inhibitor 1
- EC
- 2.7.11.22
- UniProt
- P24385, P11802, P38936
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · resolution 3.19 · 3 distinct chains · 50% helix, 6% 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 | 258 | 37% helix, 14% strand | P11802 |
| C | Cyclin-dependent kinase inhibitor 1 | protein | 54 | 37% helix, 0% strand | P38936 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.56 | 0.74 | 43 | empty |
| 2 | 67 | 0.55 | 0.87 | 14 | empty |
| 3 | 111 | 0.52 | 0.82 | 23 | empty |
| 4 | 130 | 0.48 | 0.79 | 23 | empty |
| 5 | 83 | 0.45 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1167 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1137 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 780 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6P8H · Crystal structure of CDK4 in complex with CYCLIND1 and P21 · 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 0.94
- 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
- P38936 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase inhibitor 1 (P38936) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 P38936
- Elsewhere: RCSB PDB 6P8H · PDBe 6P8H · UniProt P24385 · UniProt P11802 · UniProt P38936
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