Research workbench
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with avadomide (cc-122)
Analyse Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PSO
- Type
- protein
- Length
- 318 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, 835, ZN, PO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 108 | 8% helix, 48% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 104 | 9% helix, 50% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 106 | 6% helix, 51% strand | A4TVL0 |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · 2 copies · chains A, B
- 835 · (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione · ligand · chains C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.63 | 0.82 | 31 | empty |
| 2 | 204 | 0.51 | 0.77 | 41 | empty |
| 3 | 60 | 0.39 | 0.79 | 15 | EF2 |
| 4 | 52 | 0.35 | 0.78 | 11 | 835 |
| 5 | 68 | 0.27 | 0.73 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 613 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7PSO · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Avadomide… · the same entry in another collection · chain A against A, TM-score 1.00
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 A4TVL0
- Elsewhere: RCSB PDB 7PSO · PDBe 7PSO · UniProt A4TVL0
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