MolNFT v1 · #127655 · protein
Wt-parkin and pub complex
5N2W · E3 ubiquitin-protein ligase PARKIN,E3 ubiquitin-protein…: “Wt-parkin and pub complex”. X-ray diffraction, 4 ligands (TMO, 3CN, ZN), 5 pockets (best druggability 0.71). MolNFT v1 #127655 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N2W
- Type
- protein
- Length
- 457 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase PARKIN,E3 ubiquitin-protein ligase parkin; Polyubiquitin-B
- EC
- 2.3.2.-
- UniProt
- O60260, P0CG47
- Ligands
- TMO, 3CN, ZN, CL
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase PARKIN,E3 ubiquitin-protein ligase parkin (EC 2.3.2.-) | protein | 382 | 19% helix, 26% strand | O60260 |
| B | Polyubiquitin-B | protein | 75 | 20% helix, 36% strand | P0CG47 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 2 copies · chains A
- 3CN · 3-aminopropane · ligand · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 657 | 0.71 | 0.78 | 57 | TMO |
| 2 | 104 | 0.42 | 0.77 | 22 | empty |
| 3 | 58 | 0.38 | 0.80 | 16 | empty |
| 4 | 92 | 0.35 | 0.75 | 21 | empty |
| 5 | 52 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1427 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
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 O60260
- Every structure of UniProt P0CG47
- Elsewhere: RCSB PDB 5N2W · PDBe 5N2W · UniProt O60260 · UniProt P0CG47
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