MolNFT v1 · #115031 · protein
Crystal structure of NEDD4 with a ub variant
5C7J · E3 ubiquitin-protein ligase NEDD4: “Crystal structure of NEDD4 with a ub variant”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #115031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C7J
- Type
- protein
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4; Polyubiquitin-C
- EC
- 6.3.2.-
- UniProt
- P46934, P0CG48
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 373 | 51% helix, 13% strand | P46934 |
| B | E3 ubiquitin-protein ligase NEDD4 (EC 6.3.2.-) | protein | 373 | 51% helix, 13% strand | P46934 |
| C, D | Polyubiquitin-C | protein | 85 | 27% helix, 25% strand | P0CG48 |
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.71 | 0.84 | 46 | empty |
| 2 | 296 | 0.71 | 0.85 | 40 | empty |
| 3 | 494 | 0.67 | 0.78 | 45 | empty |
| 4 | 441 | 0.65 | 0.78 | 47 | empty |
| 5 | 324 | 0.61 | 0.78 | 50 | empty |
Interfaces
4 interfaces between chains.
- B–D · 763 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 756 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 285 Ų buried · 3 hydrogen bonds · protein-protein
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 P46934
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 5C7J · PDBe 5C7J · UniProt P46934 · UniProt P0CG48
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