MolNFT v1 · #108305 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with thalidomide
4V2Y: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with thalidomide”. X-ray diffraction, 2 ligands (EF2, ZN), 4 pockets (best druggability 0.49). MolNFT v1 #108305 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4V2Y
- Type
- protein
- Length
- 311 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, ZN
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 105 | 6% helix, 51% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 104 | 9% helix, 51% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 102 | 6% helix, 51% strand | A4TVL0 |
Ligands and binding sites
- EF2 · S-Thalidomide · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.49 | 0.80 | 23 | empty |
| 2 | 73 | 0.45 | 0.81 | 17 | empty |
| 3 | 148 | 0.40 | 0.74 | 24 | empty |
| 4 | 55 | 0.36 | 0.78 | 12 | EF2 |
Interfaces
2 interfaces between chains.
- A–B · 551 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4V2Y · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide · 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 4V2Y · PDBe 4V2Y · UniProt A4TVL0
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