Research workbench
Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin
Analyse Crystal structure of USP7 catalytic domain [V302K] 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
- 5KYD
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B; Ubiquitin carboxyl-terminal hydrolase 7
- EC
- 3.4.19.12
- UniProt
- P0CG47, Q93009
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Polyubiquitin-B | protein | 76 | 25% helix, 33% strand | P0CG47 |
| A | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 341 | 32% helix, 28% strand | Q93009 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.80 | 0.88 | 63 | empty |
| 2 | 121 | 0.41 | 0.75 | 20 | empty |
| 3 | 59 | 0.34 | 0.77 | 14 | empty |
| 4 | 77 | 0.32 | 0.74 | 22 | empty |
| 5 | 63 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- D–A · 1491 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5KYD · Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin · the same entry in another collection · chain D against D, 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 P0CG47
- Every structure of UniProt Q93009
- Elsewhere: RCSB PDB 5KYD · PDBe 5KYD · UniProt P0CG47 · UniProt Q93009
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.