Research workbench
The structure of the ubiquitin-like modifier FAT10 reveals a novel targeting mechanism for degradation by the 26S proteasome
Analyse The structure of the ubiquitin-like modifier FAT10 reveals a novel targeting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GF1
- Type
- protein
- Length
- 228 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin D
- UniProt
- O15205
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin D | protein | 78 | 23% helix, 37% strand | O15205 |
| B | Ubiquitin D | protein | 79 | 27% helix, 35% strand | O15205 |
| C | Ubiquitin D | protein | 71 | 21% helix, 39% strand | O15205 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 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 | 0.57 | 0.76 | 36 | SO4 |
| 2 | 62 | 0.32 | 0.76 | 18 | empty |
| 3 | 50 | 0.28 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 670 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 503 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GF1 · The structure of the ubiquitin-like modifier FAT10 reveals a novel targeting mechanism… · the same entry in another collection · chain B against B, TM-score 1.00
- O15205 · AlphaFold monomer V2.0 prediction for ubiquitin D (O15205) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 O15205
- Elsewhere: RCSB PDB 6GF1 · PDBe 6GF1 · UniProt O15205
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