Research workbench
Crystal structure of the first two Ubl domains of Deubiquitylase USP7
Analyse Crystal structure of the first two Ubl domains of Deubiquitylase USP7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PYZ
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.84
- Source
- Homo sapiens
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7
- EC
- 3.4.19.12
- UniProt
- Q93009
- Ligands
- UNX
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.84 · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 263 | 33% helix, 29% strand | Q93009 |
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 261 | 29% helix, 29% strand | Q93009 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.81 | 0.82 | 113 | empty |
| 2 | 77 | 0.32 | 0.74 | 18 | empty |
| 3 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4PYZ · Crystal structure of the first two ubl domains of deubiquitylase USP7 · the same entry in another collection · chain A against A, TM-score 1.00
- Q93009 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 7 (Q93009) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q93009
- Elsewhere: RCSB PDB 4PYZ · PDBe 4PYZ · UniProt Q93009
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