MolNFT v1 · #54959 · protein
Structure of USP21 in complex with linear diubiquitin-aldehyde
2Y5B · Ubiquitin carboxyl-terminal hydrolase 21: “Structure of USP21 in complex with linear diubiquitin-aldehyde”. X-ray diffraction, 2 ligands (ZN, SO4), 8 pockets (best druggability 0.80). MolNFT v1 #54959 on GenesisL1: 3D structure…
- PDB
- 2Y5B
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 21; Ubiquitin
- EC
- 3.1.2.15, 3.4.19.12
- UniProt
- Q9UK80, P0CG47
- Ligands
- ZN, SO4
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15, 3.4.19.12) | protein | 315 | 32% helix, 30% strand | Q9UK80 |
| B | Ubiquitin | protein | 150 | 22% helix, 35% strand | P0CG47 |
| E | Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15, 3.4.19.12) | protein | 325 | 33% helix, 31% strand | Q9UK80 |
| F | Ubiquitin | protein | 152 | 24% helix, 34% strand | P0CG47 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, E
- SO4 · Sulfate ion · ion · 12 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.80 | 0.81 | 93 | SO4 |
| 2 | 437 | 0.71 | 0.82 | 53 | empty |
| 3 | 386 | 0.64 | 0.78 | 50 | empty |
| 4 | 221 | 0.59 | 0.80 | 36 | empty |
| 5 | 110 | 0.49 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- E–F · 2143 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1840 Ų buried · 38 hydrogen bonds · protein-protein
- A–F · 376 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 118 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 2Y5B · Structure of USP21 in complex with linear diubiquitin-aldehyde · 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 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 P0CG47
- Elsewhere: RCSB PDB 2Y5B · PDBe 2Y5B · UniProt Q9UK80 · UniProt P0CG47
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