Research workbench
Crystal structure of the UAF1/WDR20/USP12 complex
Analyse Crystal structure of the UAF1/WDR20/USP12 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K1C
- Type
- protein
- Length
- 1,224 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 12; Wd repeat-containing protein 48; Wd…
- EC
- 3.4.19.12
- UniProt
- O75317, Q8TAF3, Q8TBZ3
- Ligands
- TAM, ZN, PO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.4.19.12) | protein | 302 | 27% helix, 30% strand | O75317 |
| B | Wd repeat-containing protein 48 | protein | 515 | 10% helix, 37% strand | Q8TAF3 |
| C | Wd repeat-containing protein 20 | protein | 407 | 2% helix, 45% strand | Q8TBZ3 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains C
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.83 | 0.84 | 93 | empty |
| 2 | 705 | 0.81 | 0.85 | 57 | empty |
| 3 | 961 | 0.77 | 0.79 | 96 | empty |
| 4 | 401 | 0.70 | 0.82 | 47 | empty |
| 5 | 249 | 0.69 | 0.84 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1127 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 416 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5K1C · Crystal structure of the UAF1/WDR20/USP12 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 0.97
- O75317 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 12 (O75317) · 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 O75317
- Every structure of UniProt Q8TAF3
- Every structure of UniProt Q8TBZ3
- Elsewhere: RCSB PDB 5K1C · PDBe 5K1C · UniProt O75317 · UniProt Q8TAF3 · UniProt Q8TBZ3
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