Research workbench
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 16B
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
- 6R1W
- Type
- protein
- Length
- 329 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- JPW, EF2, ZN, PO4
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 112 | 8% helix, 46% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 111 | 8% helix, 50% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 106 | 6% helix, 52% strand | A4TVL0 |
Ligands and binding sites
- JPW · (4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate · ligand · 2 copies · chains B, C
- EF2 · S-Thalidomide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 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 | 67 | 0.50 | 0.85 | 19 | empty |
| 2 | 125 | 0.50 | 0.80 | 27 | empty |
| 3 | 143 | 0.41 | 0.74 | 17 | empty |
| 4 | 131 | 0.40 | 0.75 | 21 | empty |
| 5 | 50 | 0.38 | 0.80 | 13 | EF2 |
Interfaces
3 interfaces between chains.
- A–B · 653 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 540 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R1W · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 16b · 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 6R1W · PDBe 6R1W · UniProt A4TVL0
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