MolNFT v1 · #129330 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with pyrrolidin-2-one (butyrolactam)
5OH2: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with pyrrolidin-2-one (butyrolactam)”. X-ray diffraction, 2 ligands (BAQ, ZN), 4 pockets (best druggability 0.50). MolNFT v1 #129330 on GenesisL1: 3D structure…
- PDB
- 5OH2
- 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
- BAQ, ZN
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 6% 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 | 6% helix, 53% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 102 | 6% helix, 50% strand | A4TVL0 |
Ligands and binding sites
- BAQ · pyrrolidin-2-one · 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 | 107 | 0.50 | 0.81 | 24 | empty |
| 2 | 128 | 0.46 | 0.78 | 22 | empty |
| 3 | 139 | 0.39 | 0.73 | 21 | empty |
| 4 | 52 | 0.35 | 0.79 | 12 | BAQ |
Interfaces
2 interfaces between chains.
- A–B · 544 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5OH2 · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Pyrrolidin-2-one… · 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 5OH2 · PDBe 5OH2 · UniProt A4TVL0
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