Research workbench
Cereblon in complex with DDB1 and cc-220
Analyse Cereblon in complex with DDB1 and cc-220 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V3O
- Type
- protein
- Length
- 1,450 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, Q96SW2
- Ligands
- 8W7, ZN
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1087 | 5% helix, 51% strand | Q16531 |
| C | Protein cereblon | protein | 363 | 29% helix, 31% strand | Q96SW2 |
Ligands and binding sites
- 8W7 · (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione · ligand · chains C
- ZN · Zinc ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.86 | 0.86 | 85 | empty |
| 2 | 783 | 0.75 | 0.80 | 77 | empty |
| 3 | 803 | 0.74 | 0.78 | 60 | empty |
| 4 | 533 | 0.73 | 0.81 | 38 | empty |
| 5 | 717 | 0.71 | 0.78 | 77 | empty |
Interfaces
1 interface between chains.
- A–C · 2250 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5V3O · Cereblon in complex with DDB1 and CC-220 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain C 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 0.85
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
- Elsewhere: RCSB PDB 5V3O · PDBe 5V3O · UniProt Q16531 · UniProt Q96SW2
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