MolNFT v1 · #162163 · protein
Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 4A and hydrolysis product
6R0S: “Cereblon isoform 4 from magnetospirillum gryphiswaldense in complex with compound 4A and hydrolysis product”. X-ray diffraction, 6 ligands (EF2, JOE, JOH), 4 pockets (best druggability 0.52). MolNFT v1 #162163 on GenesisL1: 3D…
- PDB
- 6R0S
- Type
- protein
- Length
- 324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cereblon isoform 4
- UniProt
- A4TVL0
- Ligands
- EF2, JOE, JOH, ZN, PO4, CL
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cereblon isoform 4 | protein | 109 | 8% helix, 48% strand | A4TVL0 |
| B | Cereblon isoform 4 | protein | 105 | 9% helix, 51% strand | A4TVL0 |
| C | Cereblon isoform 4 | protein | 107 | 6% helix, 50% strand | A4TVL0 |
| F | Cereblon isoform 4 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- EF2 · S-Thalidomide · ligand · chains A
- JOE · 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid · ligand · chains B
- JOH · 2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-4-nitro-isoindole-1,3-dione · ligand · chains C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- 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 | 61 | 0.52 | 0.87 | 17 | empty |
| 2 | 84 | 0.45 | 0.80 | 21 | empty |
| 3 | 146 | 0.42 | 0.75 | 24 | empty |
| 4 | 122 | 0.40 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 625 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 612 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 91 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 38 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R0S · Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 4a and… · 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 6R0S · PDBe 6R0S · UniProt A4TVL0
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