Research workbench
Crystal structure of covalent ubiquitin-USP21 complex
Analyse Crystal structure of covalent ubiquitin-USP21 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I3T
- Type
- protein
- Length
- 1,527 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 21; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- Q9UK80, P62988
- Ligands
- NEH, ZN
- Pockets
- 18 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) | protein | 303 | 35% helix, 30% strand | Q9UK80 |
| C, E | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) | protein | 310 | 34% helix, 29% strand | Q9UK80 |
| G | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) | protein | 304 | 34% helix, 29% strand | Q9UK80 |
| B, D, F, H | Ubiquitin | protein | 75 | 20% helix, 32% strand | P62988 |
Ligands and binding sites
- NEH · Ethanamine · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.77 | 0.79 | 82 | empty |
| 2 | 671 | 0.75 | 0.81 | 72 | empty |
| 3 | 53 | 0.70 | 0.98 | 22 | empty |
| 4 | 51 | 0.69 | 0.98 | 23 | empty |
| 5 | 332 | 0.67 | 0.81 | 34 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1850 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1846 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 1835 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 682 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3I3T · Crystal structure of covalent ubiquitin-USP21 complex · the same entry in another collection · chain H against H, 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 A 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 3I3T · PDBe 3I3T · UniProt Q9UK80 · UniProt P62988
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