Research workbench
USP15 catalytic domain in complex with small molecule
Analyse USP15 catalytic domain in complex with small molecule in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GH9
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 15
- EC
- 3.4.19.12
- UniProt
- Q9Y4E8
- Ligands
- MIX, ZN
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 331 | 28% helix, 28% strand | Q9Y4E8 |
| B | Ubiquitin carboxyl-terminal hydrolase 15 (EC 3.4.19.12) | protein | 309 | 29% helix, 27% strand | Q9Y4E8 |
Ligands and binding sites
- MIX · 1,4-dihydroxy-5,8-bis({2-[(2-hydroxyethyl) amino]ethyl}amino)-9,10-anthracenedione · ligand · chains A
- ZN · Zinc ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.55 | 0.76 | 37 | empty |
| 2 | 164 | 0.47 | 0.76 | 30 | empty |
| 3 | 89 | 0.42 | 0.79 | 22 | empty |
| 4 | 118 | 0.40 | 0.75 | 32 | empty |
| 5 | 82 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 696 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6GH9 · USP15 catalytic domain in complex with small molecule · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.98
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 6GH9 · PDBe 6GH9 · UniProt Q9Y4E8
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