MolNFT v1 · #68529 · protein
Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)
3JYU · Ubiquitin carboxyl-terminal hydrolase: “Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4)”. X-ray diffraction, 1 ligand (1PS), 4 pockets (best druggability 0.81). MolNFT v1 #68529 on GenesisL1…
- PDB
- 3JYU
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase
- EC
- 3.1.2.15
- UniProt
- Q921M8
- Ligands
- 1PS
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase (EC 3.1.2.15) | protein | 220 | 22% helix, 29% strand | Q921M8 |
| B | Ubiquitin carboxyl-terminal hydrolase (EC 3.1.2.15) | protein | 216 | 23% helix, 29% strand | Q921M8 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.81 | 0.82 | 82 | empty |
| 2 | 201 | 0.55 | 0.79 | 31 | empty |
| 3 | 53 | 0.30 | 0.76 | 15 | empty |
| 4 | 56 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3JYU · Crystal structure of the N-terminal domains of the ubiquitin specific peptidase 4 (USP4) · the same entry in another collection · chain A against A, TM-score 1.00
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 Q921M8
- Elsewhere: RCSB PDB 3JYU · PDBe 3JYU · UniProt Q921M8
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