Research workbench
Crystal structure of human USP2 C276S mutant in complex with ubiquitin
Analyse Crystal structure of human USP2 C276S mutant in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVE
- Type
- protein
- Length
- 407 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 2; Ubiquitin-40S ribosomal protein S27A
- EC
- 3.4.19.12
- UniProt
- O75604, P62992
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.4.19.12) | protein | 331 | 31% helix, 29% strand | O75604 |
| B | Ubiquitin-40S ribosomal protein S27A | protein | 76 | 25% helix, 33% strand | P62992 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.67 | 0.80 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2072 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 5XVE · Crystal structure of human USP2 C276S mutant in complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- O75604 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 2 (O75604) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 O75604
- Every structure of UniProt P62992
- Elsewhere: RCSB PDB 5XVE · PDBe 5XVE · UniProt O75604 · UniProt P62992
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