MolNFT v1 · #191337 · protein
CEREBLON~DDB1 in the apo form with DDB1 in the hinged conformation
8D7X · DNA damage-binding protein 1: “CEREBLON~DDB1 in the apo form with DDB1 in the hinged conformation”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #191337 on GenesisL1: 3D structure, binding sites…
- PDB
- 8D7X
- Type
- protein
- Length
- 1,484 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA damage-binding protein 1; Protein cereblon
- UniProt
- Q16531, Q96SW2
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA damage-binding protein 1 | protein | 1135 | 5% helix, 44% strand | Q16531 |
| B | Protein cereblon | protein | 349 | 26% helix, 30% strand | Q96SW2 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.85 | 0.86 | 92 | empty |
| 2 | 1166 | 0.81 | 0.83 | 152 | empty |
| 3 | 1127 | 0.81 | 0.82 | 106 | empty |
| 4 | 292 | 0.74 | 0.87 | 60 | empty |
| 5 | 385 | 0.71 | 0.83 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 2376 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 8D7X · Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.87
- Q96SW2 · AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 8D7X · PDBe 8D7X · UniProt Q16531 · UniProt Q96SW2
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