MolNFT v1 · #53989 · protein
NEDD4 HECT:UB complex
2XBB · E3 ubiquitin-protein ligase NEDD4: “NEDD4 HECT:UB complex”. X-ray diffraction, 9 pockets (best druggability 0.66). MolNFT v1 #53989 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XBB
- Type
- protein
- Length
- 902 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4; Ubiquitin
- EC
- 6.3.2.-
- UniProt
- P46934, P0CG53
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 375 | 49% helix, 13% strand | P46934 |
| C, D | Ubiquitin | protein | 76 | 24% helix, 33% strand | P0CG53 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.66 | 0.77 | 55 | empty |
| 2 | 362 | 0.62 | 0.78 | 40 | empty |
| 3 | 313 | 0.61 | 0.79 | 41 | empty |
| 4 | 290 | 0.56 | 0.76 | 49 | empty |
| 5 | 310 | 0.56 | 0.76 | 42 | empty |
Interfaces
5 interfaces between chains.
- A–C · 939 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 916 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 222 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 139 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2XBB · Nedd4 HECT:Ub complex · the same entry in another collection · chain A against A, TM-score 1.00
- P0CG53 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG53) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P46934 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NEDD4 (P46934) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 P46934
- Every structure of UniProt P0CG53
- Elsewhere: RCSB PDB 2XBB · PDBe 2XBB · UniProt P46934 · UniProt P0CG53
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.