Research workbench
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with a benzotriazole analog of thalidomide
Analyse Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PJK
- Type
- protein
- Length
- 265 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- 7SE, ZN
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cereblon isoform 4 | protein | 105 | 6% helix, 51% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 55 | 5% helix, 44% strand | A4TVL0 |
Ligands and binding sites
- 7SE · (3S)-3-(benzotriazol-2-yl)piperidine-2,6-dione · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.50 | 0.75 | 31 | empty |
| 2 | 73 | 0.41 | 0.79 | 17 | empty |
| 3 | 57 | 0.39 | 0.80 | 14 | 7SE |
Interfaces
2 interfaces between chains.
- A–B · 576 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 348 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7PJK · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with a benzotriazole… · 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 7PJK · PDBe 7PJK · UniProt A4TVL0
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