Research workbench
Crystal structure of human cereblon in complex with DDB1 and lenalidomide
Analyse Crystal structure of human cereblon in complex with DDB1 and lenalidomide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TZ4
- Type
- protein
- Length
- 1,431 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
- LVY, ZN
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1070 | 6% helix, 52% strand | Q16531 |
| C | Protein cereblon | protein | 361 | 26% helix, 34% strand | Q96SW2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.86 | 0.87 | 91 | empty |
| 2 | 765 | 0.76 | 0.80 | 76 | empty |
| 3 | 832 | 0.76 | 0.80 | 86 | empty |
| 4 | 823 | 0.74 | 0.79 | 64 | empty |
| 5 | 584 | 0.74 | 0.81 | 38 | empty |
Interfaces
1 interface between chains.
- A–C · 2279 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4TZ4 · Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide · 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 0.82
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 4TZ4 · PDBe 4TZ4 · UniProt Q16531 · UniProt Q96SW2
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