Research workbench
Crystal structure of human USP46-WDR48-WDR20 complex
Analyse Crystal structure of human USP46-WDR48-WDR20 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JLQ
- Type
- protein
- Length
- 1,205 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 46; Wd repeat-containing protein 48; Wd…
- EC
- 3.4.19.12
- UniProt
- P62068, Q8TAF3, Q8TBZ3, B3KQX8, L8I535
- Ligands
- ZN, PO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.4.19.12) | protein | 292 | 28% helix, 32% strand | P62068 |
| B | Wd repeat-containing protein 48 | protein | 512 | 11% helix, 42% strand | Q8TAF3 |
| C | Wd repeat-containing protein 20,HIGHLY similar to wd repeat protein 20,WD repeat-containing protein 20 | protein | 401 | 3% helix, 47% strand | Q8TBZ3, B3KQX8, L8I535 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.82 | 0.83 | 98 | empty |
| 2 | 723 | 0.81 | 0.84 | 64 | empty |
| 3 | 323 | 0.79 | 0.89 | 40 | empty |
| 4 | 838 | 0.75 | 0.79 | 78 | empty |
| 5 | 426 | 0.71 | 0.82 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1124 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 776 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 347 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6JLQ · Crystal structure of human USP46-WDR48-WDR20 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 B against A, TM-score 0.99
- Q8TBZ3 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 20 (Q8TBZ3) · a predicted model of the same protein · chain C 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 A against A, TM-score 0.93
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 P62068
- Every structure of UniProt Q8TAF3
- Every structure of UniProt Q8TBZ3
- Every structure of UniProt B3KQX8
- Every structure of UniProt L8I535
- Elsewhere: RCSB PDB 6JLQ · PDBe 6JLQ · UniProt P62068 · UniProt Q8TAF3 · UniProt Q8TBZ3 · UniProt B3KQX8 · UniProt L8I535
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