Research workbench
Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin
Analyse Crystal structure of USP7 catalytic domain [L299A] mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KYF
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Homo sapiens
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q93009, P0CG47
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.45 · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 340 | 33% helix, 30% strand | Q93009 |
| C | Polyubiquitin-B | protein | 76 | 24% helix, 30% strand | P0CG47 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.51 | 0.86 | 22 | empty |
| 2 | 92 | 0.41 | 0.77 | 16 | empty |
| 3 | 106 | 0.37 | 0.74 | 23 | GOL |
| 4 | 70 | 0.35 | 0.76 | 14 | empty |
| 5 | 54 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- B–C · 1892 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 5KYF · Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin · the same entry in another collection · chain B against B, 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 0.97
- P0CG47 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG47) · a predicted model of the same protein · chain C against A, TM-score 0.92
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
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5KYF · PDBe 5KYF · UniProt Q93009 · UniProt P0CG47
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