Research workbench
Structure of the USP15 deubiquitinase domain in complex with a third- generation inhibitory ubv
Analyse Structure of the USP15 deubiquitinase domain in complex with a third… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CPM
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 15; Ubiquitin variant 15.1D
- EC
- 3.4.19.12
- UniProt
- Q9Y4E8
- Ligands
- CA, NA, ZN
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 339 | 28% helix, 27% strand | Q9Y4E8 |
| D | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 332 | 30% helix, 28% strand | Q9Y4E8 |
| E | Ubiquitin variant 15.1D | protein | 79 | 23% helix, 39% strand | — |
| F | Ubiquitin variant 15.1D | protein | 78 | 23% helix, 40% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains C, D, E
- NA · Sodium ion · metal · 3 copies · chains C, D, F
- ZN · Zinc ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · 3 copies · chains C, F, D, E
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.80 | 0.81 | 88 | GOL |
| 2 | 1166 | 0.80 | 0.81 | 87 | CA, GOL |
| 3 | 737 | 0.73 | 0.79 | 45 | CA |
| 4 | 57 | 0.25 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–F · 973 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 961 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 587 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6CPM · Structure of the USP15 deubiquitinase domain in complex with a third-generation… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9Y4E8 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 15 (Q9Y4E8) · a predicted model of the same protein · chain D 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 Q9Y4E8
- Elsewhere: RCSB PDB 6CPM · PDBe 6CPM · UniProt Q9Y4E8
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