Research workbench
Crystal structure of a CDC6 phosphopeptide in complex with CKS1
Analyse Crystal structure of a CDC6 phosphopeptide in complex with CKS1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LPA
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinases regulatory subunit
- UniProt
- P20486
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclin-dependent kinases regulatory subunit | protein | 113 | 21% helix, 20% strand | P20486 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.66 | 0.76 | 73 | empty |
| 2 | 124 | 0.53 | 0.81 | 23 | empty |
| 3 | 75 | 0.51 | 0.84 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 737 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 675 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 118 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 105 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 4LPA · Crystal structure of a Cdc6 phosphopeptide in complex with Cks1 · the same entry in another collection · chain D against D, TM-score 1.00
- P20486 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinases regulatory subunit (P20486) · a predicted model of the same protein · chain D against A, TM-score 0.89
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 P20486
- Elsewhere: RCSB PDB 4LPA · PDBe 4LPA · UniProt P20486
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