Research workbench
Crystal structure of a josephin-ubiquitin complex: evolutionary restraints on ataxin-3 deubiquitinating activity
Analyse Crystal structure of a josephin-ubiquitin complex: evolutionary restraints on… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O65
- Type
- protein
- Length
- 1,031 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ataxin-3-like protein; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- Q9H3M9, P0CG47
- Ligands
- NEH, NA
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Putative ataxin-3-like protein (EC 3.1.2.15) | protein | 181 | 41% helix, 19% strand | Q9H3M9 |
| B, D, F, H | Ubiquitin | protein | 75 | 24% helix, 36% strand | P0CG47 |
| C | Putative ataxin-3-like protein (EC 3.1.2.15) | protein | 182 | 38% helix, 18% strand | Q9H3M9 |
| E | Putative ataxin-3-like protein (EC 3.1.2.15) | protein | 187 | 37% helix, 17% strand | Q9H3M9 |
Ligands and binding sites
- NEH · Ethanamine · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.72 | 0.76 | 94 | NEH |
| 2 | 137 | 0.66 | 0.87 | 20 | empty |
| 3 | 133 | 0.62 | 0.86 | 24 | empty |
| 4 | 118 | 0.61 | 0.86 | 28 | empty |
| 5 | 162 | 0.61 | 0.83 | 24 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1342 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1322 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1286 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1195 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 762 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified, 8 covalent (engineered, covalent ligand).
Compared structures
- 3O65 · Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9H3M9 · AlphaFold monomer V2.0 prediction for ataxin-3-like protein (Q9H3M9) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9H3M9
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 3O65 · PDBe 3O65 · UniProt Q9H3M9 · UniProt P0CG47
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