MolNFT v1 · #95590 · protein
Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
4IUM: “Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin”. X-ray diffraction, 2 ligands (3CN, ZN), 2 pockets (best druggability 0.34). MolNFT v1 #95590 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4IUM
- Type
- protein
- Length
- 202 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease 2; Ubiquitin
- EC
- 3.4.22.-
- UniProt
- P19811, P0CG48
- Ligands
- 3CN, ZN
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease 2 (EC 3.4.22.-) | protein | 127 | 29% helix, 19% strand | P19811 |
| B | Ubiquitin | protein | 75 | 25% helix, 35% strand | P0CG48 |
Ligands and binding sites
- 3CN · 3-aminopropane · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.34 | 0.75 | 17 | GOL |
| 2 | 55 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 714 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4IUM · Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin · the same entry in another collection · chain A against A, 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 P19811
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4IUM · PDBe 4IUM · UniProt P19811 · UniProt P0CG48
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