Research workbench
WDR48 (2-580):USP46~UBIQUITIN ternary complex
Analyse WDR48 (2-580):USP46~UBIQUITIN ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CVN
- Type
- protein
- Length
- 911 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 48; Ubiquitin carboxyl-terminal hydrolase 46; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q8TAF3, P62068, P0CG47
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 48 | protein | 514 | 10% helix, 41% strand | Q8TAF3 |
| B | Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.4.19.12) | protein | 321 | 29% helix, 35% strand | P62068 |
| D | Polyubiquitin-B | protein | 76 | 16% helix, 30% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.81 | 0.85 | 57 | empty |
| 2 | 1013 | 0.77 | 0.80 | 80 | empty |
| 3 | 135 | 0.56 | 0.82 | 18 | empty |
| 4 | 212 | 0.51 | 0.76 | 24 | empty |
| 5 | 152 | 0.47 | 0.77 | 30 | empty |
Interfaces
2 interfaces between chains.
- B–D · 1942 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 790 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5CVN · WDR48 (2-580):USP46~ubiquitin ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TAF3 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 48 (Q8TAF3) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P62068 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 46 (P62068) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8TAF3
- Every structure of UniProt P62068
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5CVN · PDBe 5CVN · UniProt Q8TAF3 · UniProt P62068 · UniProt P0CG47
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