Research workbench
NEDD4 hect-UB:UB complex
Analyse NEDD4 hect-UB:UB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BBN
- Type
- protein
- Length
- 530 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4; Polyubiquitin-B
- EC
- 6.3.2.-
- UniProt
- P46934, P0CG53
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 378 | 50% helix, 14% strand | P46934 |
| C | Polyubiquitin-B | protein | 76 | 18% helix, 30% strand | P0CG53 |
| F | Polyubiquitin-B | protein | 76 | 20% helix, 37% strand | P0CG53 |
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 | 451 | 0.66 | 0.78 | 46 | empty |
| 2 | 556 | 0.63 | 0.75 | 52 | empty |
| 3 | 176 | 0.60 | 0.82 | 33 | empty |
| 4 | 150 | 0.45 | 0.76 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1006 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 812 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4BBN · NEDD4 HECT-Ub: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 F 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 0.74
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 4BBN · PDBe 4BBN · UniProt P46934 · UniProt P0CG53
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