Research workbench
USP28 catalytic domain apo
Analyse USP28 catalytic domain apo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H4I
- Type
- protein
- Length
- 907 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 28
- EC
- 3.4.19.12
- UniProt
- Q96RU2
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12) | protein | 456 | 48% helix, 20% strand | Q96RU2 |
| C | Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12) | protein | 451 | 47% helix, 21% strand | Q96RU2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.75 | 0.86 | 47 | empty |
| 2 | 555 | 0.73 | 0.81 | 58 | empty |
| 3 | 328 | 0.73 | 0.85 | 45 | empty |
| 4 | 474 | 0.59 | 0.74 | 40 | SO4 |
| 5 | 79 | 0.58 | 0.88 | 22 | empty |
Interfaces
1 interface between chains.
- A–C · 833 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
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 Q96RU2
- Elsewhere: RCSB PDB 6H4I · PDBe 6H4I · UniProt Q96RU2
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