MolNFT v1 · #108306 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with pomalidomide
4V2Z: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with pomalidomide”. X-ray diffraction, 2 ligands (Y70, ZN), 4 pockets (best druggability 0.61). MolNFT v1 #108306 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4V2Z
- Type
- protein
- Length
- 310 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- Y70, ZN
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 51% 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 | 100 | 6% helix, 51% strand | A4TVL0 |
Ligands and binding sites
- Y70 · S-Pomalidomide · ligand · 3 copies · chains A, B, C
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.61 | 0.82 | 27 | empty |
| 2 | 74 | 0.43 | 0.80 | 19 | empty |
| 3 | 53 | 0.38 | 0.80 | 15 | Y70 |
| 4 | 70 | 0.29 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 550 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4V2Z · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pomalidomide · 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 4V2Z · PDBe 4V2Z · UniProt A4TVL0
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