Research workbench
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 11A
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
- 6R18
- Type
- protein
- Length
- 329 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, JOQ, ZN, PO4, CL
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 111 | 8% helix, 47% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 109 | 8% helix, 49% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 106 | 6% helix, 52% strand | A4TVL0 |
| D | Cereblon isoform 4 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · 2 copies · chains A, C, D
- JOQ · [4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate · ligand · chains B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A, B
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 | 302 | 0.60 | 0.79 | 54 | empty |
| 2 | 63 | 0.43 | 0.81 | 14 | EF2 |
| 3 | 145 | 0.41 | 0.75 | 16 | empty |
| 4 | 52 | 0.38 | 0.80 | 14 | EF2 |
Interfaces
4 interfaces between chains.
- A–B · 646 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 565 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R18 · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a · 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 6R18 · PDBe 6R18 · UniProt A4TVL0
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