MolNFT v1 · #123978 · protein
Crystal structure of the UAF1/USP12 complex in F222 space group
5K1B · Wd repeat-containing protein 48: “Crystal structure of the UAF1/USP12 complex in F222 space group”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.80). MolNFT v1 #123978 on GenesisL1: 3D structure, binding sites…
- PDB
- 5K1B
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 48; Ubiquitin carboxyl-terminal hydrolase 12
- EC
- 3.4.19.12
- UniProt
- Q8TAF3, O75317
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Wd repeat-containing protein 48 | protein | 579 | 12% helix, 38% strand | Q8TAF3 |
| A | Ubiquitin carboxyl-terminal hydrolase 12 (EC 3.4.19.12) | protein | 264 | 28% helix, 32% strand | O75317 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.80 | 0.83 | 58 | empty |
| 2 | 291 | 0.60 | 0.79 | 32 | empty |
| 3 | 97 | 0.54 | 0.84 | 20 | empty |
| 4 | 235 | 0.53 | 0.76 | 36 | empty |
| 5 | 123 | 0.49 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- B–A · 750 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5K1B · Crystal structure of the UAF1/USP12 complex in F222 space group · the same entry in another collection · chain B against B, 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 0.98
- 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 0.91
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 O75317
- Elsewhere: RCSB PDB 5K1B · PDBe 5K1B · UniProt Q8TAF3 · UniProt O75317
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