Research workbench
Notch ligand, jagged-1, contains an N-terminal C2 domain
Analyse Notch ligand, jagged-1, contains an N-terminal C2 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CBZ
- Type
- protein
- Length
- 543 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein jagged-1
- UniProt
- P78504
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein jagged-1 | protein | 291 | 2% helix, 41% strand | P78504 |
| B | Protein jagged-1 | protein | 252 | 0% helix, 44% strand | P78504 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.60 | 0.76 | 62 | empty |
| 2 | 181 | 0.53 | 0.78 | 27 | empty |
| 3 | 150 | 0.49 | 0.78 | 24 | empty |
| 4 | 85 | 0.33 | 0.74 | 22 | empty |
| 5 | 71 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1231 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 3 glycan (disulfide, N-glycosylation, O-glycosylation).
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 P78504
- Elsewhere: RCSB PDB 4CBZ · PDBe 4CBZ · UniProt P78504
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