Research workbench
Crystal structure of USP30 (C77A) in complex with LYS6-linked diubiquitin
Analyse Crystal structure of USP30 (C77A) in complex with LYS6-linked diubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OHP
- Type
- protein
- Length
- 465 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 30; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q70CQ3, P0CG47
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 30 (EC 3.4.19.12) | protein | 315 | 26% helix, 33% strand | Q70CQ3 |
| B | Polyubiquitin-B | protein | 76 | 20% helix, 32% strand | P0CG47 |
| C | Polyubiquitin-B | protein | 74 | 26% helix, 36% strand | P0CG47 |
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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.73 | 0.97 | 30 | empty |
| 2 | 141 | 0.52 | 0.80 | 26 | empty |
| 3 | 184 | 0.50 | 0.77 | 28 | empty |
| 4 | 185 | 0.47 | 0.76 | 35 | empty |
| 5 | 65 | 0.38 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1752 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 58 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5OHP · Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- Q70CQ3 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 30 (Q70CQ3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q70CQ3
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5OHP · PDBe 5OHP · UniProt Q70CQ3 · UniProt P0CG47
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