Research workbench
Crystal structure of the C2 domain of the E3 ubiquitin- protein ligase NEDD4
Analyse Crystal structure of the C2 domain of the E3 ubiquitin- protein ligase NEDD4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B7Y
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4
- EC
- 6.3.2.-
- UniProt
- P46934
- Ligands
- CA
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 144 | 0% helix, 47% strand | P46934 |
| B | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 146 | 2% helix, 46% strand | P46934 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.48 | 0.76 | 34 | empty |
| 2 | 53 | 0.32 | 0.77 | 15 | empty |
| 3 | 69 | 0.31 | 0.74 | 16 | empty |
| 4 | 75 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 222 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3B7Y · Crystal structure of the C2 Domain of the E3 Ubiquitin-Protein Ligase NEDD4 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.38
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
- Elsewhere: RCSB PDB 3B7Y · PDBe 3B7Y · UniProt P46934
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