Research workbench
Structural basis of lenalidomide induced CK1A degradation by the CRL4CRBN ubiquitin ligase
Analyse Structural basis of lenalidomide induced CK1A degradation by the CRL4CRBN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FQD
- Type
- protein
- Length
- 2,915 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein cereblon; Casein kinase I isoform alpha
- EC
- 6.3.2.19
- UniProt
- Q16531, Q96SW2, P48729
- Ligands
- LVY, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 (EC 6.3.2.19) | protein | 789 | 7% helix, 52% strand | Q16531 |
| B | Protein cereblon | protein | 381 | 28% helix, 34% strand | Q96SW2 |
| C, F | Casein kinase I isoform alpha | protein | 294 | 38% helix, 18% strand | P48729 |
| D | DNA damage-binding protein 1 (EC 6.3.2.19) | protein | 790 | 7% helix, 52% strand | Q16531 |
| E | Protein cereblon | protein | 367 | 26% helix, 32% strand | Q96SW2 |
Ligands and binding sites
- LVY · S-Lenalidomide · ligand · 2 copies · chains B, C, E, F
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.87 | 0.88 | 84 | empty |
| 2 | 1103 | 0.86 | 0.87 | 90 | empty |
| 3 | 1134 | 0.82 | 0.83 | 119 | empty |
| 4 | 877 | 0.82 | 0.84 | 98 | empty |
| 5 | 1062 | 0.73 | 0.76 | 101 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2530 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 2506 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 651 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 630 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 628 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5FQD · Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase · the same entry in another collection · chain F against F, TM-score 1.00
- P48729 · AlphaFold monomer V2.0 prediction for casein kinase I isoform alpha (P48729) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q16531 · AlphaFold monomer V2.0 prediction for DNA damage-binding protein 1 (Q16531) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q16531
- Every structure of UniProt Q96SW2
- Every structure of UniProt P48729
- Elsewhere: RCSB PDB 5FQD · PDBe 5FQD · UniProt Q16531 · UniProt Q96SW2 · UniProt P48729
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