MolNFT v1 · #47065 · protein
Catalytic domain of the human NEDD4-like E3 ligase
2ONI · E3 ubiquitin-protein ligase NEDD4-like protein: “Catalytic domain of the human NEDD4-like E3 ligase”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.63). MolNFT v1 #47065 on GenesisL1: 3D structure, binding sites…
- PDB
- 2ONI
- Type
- protein
- Length
- 377 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4-like protein
- EC
- 6.3.2.-
- UniProt
- Q96PU5
- Ligands
- NA
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase NEDD4-like protein (EC 6.3.2.-) | protein | 377 | 51% helix, 14% strand | Q96PU5 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.63 | 0.80 | 31 | empty |
| 2 | 372 | 0.57 | 0.75 | 35 | empty |
| 3 | 175 | 0.55 | 0.80 | 32 | empty |
| 4 | 87 | 0.36 | 0.75 | 24 | empty |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 2ONI · Catalytic Domain of the Human NEDD4-like E3 Ligase · the same entry in another collection · chain A against A, TM-score 1.00
- Q96PU5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NEDD4-like (Q96PU5) · a predicted model of the same protein · chain A against A, TM-score 0.69
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 Q96PU5
- Elsewhere: RCSB PDB 2ONI · PDBe 2ONI · UniProt Q96PU5
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