Research workbench
USP28 catalytic domain variant E593D in complex with ubpa
Analyse USP28 catalytic domain variant E593D in complex with ubpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H4H
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 28; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q96RU2, P0CG47
- Ligands
- AYE, SO4
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12) | protein | 458 | 47% helix, 21% strand | Q96RU2 |
| B | Ubiquitin carboxyl-terminal hydrolase 28 (EC 3.4.19.12) | protein | 420 | 47% helix, 21% strand | Q96RU2 |
| C, D | Polyubiquitin-B | protein | 75 | 24% helix, 32% strand | P0CG47 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.73 | 0.76 | 84 | empty |
| 2 | 306 | 0.66 | 0.82 | 32 | empty |
| 3 | 142 | 0.62 | 0.85 | 21 | empty |
| 4 | 316 | 0.60 | 0.78 | 42 | empty |
| 5 | 293 | 0.58 | 0.77 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1616 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1569 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 980 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6H4H · Usp28 catalytic domain variant E593D in complex with UbPA · the same entry in another collection · chain A against A, TM-score 1.00
- Q96RU2 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 28 (Q96RU2) · 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 Q96RU2
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 6H4H · PDBe 6H4H · UniProt Q96RU2 · UniProt P0CG47
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