MolNFT v1 · #125084 · protein
Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound)
5KYC · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound)”. X-ray diffraction, 6 pockets (best druggability 0.82). MolNFT v1 #125084 on GenesisL1…
- PDB
- 5KYC
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7; Polyubiquitin-B
- EC
- 3.4.19.12
- UniProt
- Q93009, P0CG47
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.4.19.12) | protein | 340 | 34% helix, 27% strand | Q93009 |
| C | Polyubiquitin-B | protein | 76 | 20% helix, 28% strand | P0CG47 |
Ligands and binding sites
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 | 809 | 0.82 | 0.85 | 72 | MLA |
| 2 | 118 | 0.41 | 0.75 | 18 | empty |
| 3 | 92 | 0.38 | 0.76 | 18 | empty |
| 4 | 73 | 0.34 | 0.76 | 12 | empty |
| 5 | 59 | 0.33 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- B–C · 1277 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5KYC · Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin… · the same entry in another collection · chain B against B, 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 Q93009
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5KYC · PDBe 5KYC · UniProt Q93009 · UniProt P0CG47
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