Research workbench
Structure of the DDB1-crbn E3 ubiquitin ligase bound to thalidomide
Analyse Structure of the DDB1-crbn E3 ubiquitin ligase bound to thalidomide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CI1
- Type
- protein
- Length
- 1,461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein cereblon
- UniProt
- Q16531, P0CF65
- Ligands
- EF2, ZN
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1091 | 5% helix, 53% strand | Q16531 |
| B | Protein cereblon | protein | 370 | 26% helix, 34% strand | P0CF65 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.86 | 0.87 | 83 | empty |
| 2 | 1160 | 0.81 | 0.82 | 112 | empty |
| 3 | 942 | 0.80 | 0.82 | 91 | empty |
| 4 | 781 | 0.73 | 0.78 | 57 | empty |
| 5 | 519 | 0.72 | 0.81 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2365 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4CI1 · Structure of the DDB1-CRBN E3 ubiquitin ligase bound to thalidomide · the same entry in another collection · chain A against A, TM-score 1.00
- P0CF65 · AlphaFold monomer V2.0 prediction for protein cereblon (P0CF65) · 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 0.96
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 P0CF65
- Elsewhere: RCSB PDB 4CI1 · PDBe 4CI1 · UniProt Q16531 · UniProt P0CF65
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