MolNFT v1 · #115843 · protein
WDR48:USP46~UBIQUITIN ternary complex
5CVO · Wd repeat-containing protein 48: “WDR48:USP46~UBIQUITIN ternary complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #115843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CVO
- Type
- protein
- Length
- 2,015 residues
- Chains
- 6
- 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
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 48 | protein | 609 | 13% helix, 36% strand | Q8TAF3 |
| B, E | Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.4.19.12) | protein | 321 | 30% helix, 34% strand | P62068 |
| C, F | Polyubiquitin-B | protein | 76 | 20% helix, 32% strand | P0CG47 |
| D | Wd repeat-containing protein 48 | protein | 612 | 13% helix, 36% strand | Q8TAF3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.81 | 0.84 | 55 | empty |
| 2 | 682 | 0.81 | 0.85 | 56 | empty |
| 3 | 799 | 0.80 | 0.83 | 77 | empty |
| 4 | 935 | 0.79 | 0.81 | 74 | empty |
| 5 | 667 | 0.72 | 0.79 | 77 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1996 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1991 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 828 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 769 Ų buried · 18 hydrogen bonds · protein-protein
- B–E · 489 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5CVO · WDR48:USP46~ubiquitin ternary complex · the same entry in another collection · chain F against F, 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 0.97
- 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 5CVO · PDBe 5CVO · UniProt Q8TAF3 · UniProt P62068 · UniProt P0CG47
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