MolNFT v1 · #129351 · protein
Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution)
5OHN · Ubiquitin carboxyl-terminal hydrolase 30,UBIQUITIN…: “Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution)”. X-ray diffraction, 2 ligands (AYE, ZN), 9 pockets (best druggability 0.76). MolNFT…
- PDB
- 5OHN
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 30,UBIQUITIN carboxyl-terminal hydrolase 30…
- EC
- 3.4.19.12
- UniProt
- Q70CQ3, P0CG47
- Ligands
- AYE, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 30,UBIQUITIN carboxyl-terminal hydrolase 30 (EC 3.4.19.12) | protein | 299 | 28% helix, 33% strand | Q70CQ3 |
| B, D | Polyubiquitin-B | protein | 75 | 20% helix, 31% strand | P0CG47 |
| C | Ubiquitin carboxyl-terminal hydrolase 30,UBIQUITIN carboxyl-terminal hydrolase 30 (EC 3.4.19.12) | protein | 297 | 28% helix, 33% strand | Q70CQ3 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.76 | 0.80 | 90 | empty |
| 2 | 53 | 0.71 | 0.98 | 22 | empty |
| 3 | 179 | 0.47 | 0.76 | 33 | empty |
| 4 | 149 | 0.46 | 0.77 | 25 | empty |
| 5 | 90 | 0.39 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1587 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1586 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 691 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5OHN · Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low… · 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 C 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 5OHN · PDBe 5OHN · UniProt Q70CQ3 · UniProt P0CG47
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