MolNFT v1 · #81902 · protein
Crystal structure of USP2 in complex with mutated ubiquitin
3V6C · Ubiquitin carboxyl-terminal hydrolase 2: “Crystal structure of USP2 in complex with mutated ubiquitin”. X-ray diffraction, 2 ligands (ZN, CL), 1 pocket (best druggability 0.68). MolNFT v1 #81902 on GenesisL1: 3D structure, binding…
- PDB
- 3V6C
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 2; Ubiquitin
- EC
- 3.4.19.12
- UniProt
- O75604, P0CG48
- Ligands
- ZN, CL
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 2 (EC 3.4.19.12) | protein | 327 | 31% helix, 27% strand | O75604 |
| B | Ubiquitin | protein | 81 | 22% helix, 31% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
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 | 354 | 0.68 | 0.81 | 42 | GOL |
Interfaces
1 interface between chains.
- A–B · 1939 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 3V6C · Crystal Structure of USP2 in complex with mutated 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 0.98
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 P0CG48
- Elsewhere: RCSB PDB 3V6C · PDBe 3V6C · UniProt O75604 · UniProt P0CG48
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