Research workbench
USP21 in complex with a ubiquitin-based, USP21-specific inhibitor
Analyse USP21 in complex with a ubiquitin-based, USP21-specific inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MTN
- Type
- protein
- Length
- 784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 21; Ubiquitin variant UBV.21.4
- EC
- 3.1.2.15
- UniProt
- Q9UK80, P62988
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) | protein | 316 | 33% helix, 29% strand | Q9UK80 |
| B, D | Ubiquitin variant UBV.21.4 | protein | 77 | 23% helix, 32% strand | P62988 |
| C | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) | protein | 314 | 32% helix, 28% strand | Q9UK80 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.78 | 0.82 | 83 | GOL |
| 2 | 828 | 0.76 | 0.80 | 71 | GOL |
| 3 | 94 | 0.51 | 0.83 | 19 | empty |
| 4 | 110 | 0.51 | 0.82 | 17 | empty |
| 5 | 57 | 0.33 | 0.77 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1858 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 382 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 207 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3MTN · Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UK80 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 21 (Q9UK80) · 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 Q9UK80
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 3MTN · PDBe 3MTN · UniProt Q9UK80 · UniProt P62988
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