Complex of NOTCH1 (EGF11-13) bound to delta-like 4 (N-EGF1)

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 40% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, E, D, A
• BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B, D, E
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B, D, E
• CA · Calcium ion · metal · 6 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–E · 1365 Ų buried · 12 hydrogen bonds · protein-protein
• D–E · 1014 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 1006 Ų buried · 9 hydrogen bonds · protein-protein
• A–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
• A–E · 17 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide, 14 glycan, 12 modified (disulfide, methylation, O-glycosylation, N-glycosylation).

Compared structures

• 4XL1 · Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1) · the same entry in another collection · chain E against E, TM-score 1.00
• D3ZHH1 · AlphaFold monomer V2.0 prediction for delta-like protein 4 (D3ZHH1) · a predicted model of the same protein · chain B against A, TM-score 0.88
• Q07008 · AlphaFold monomer V2.0 prediction for neurogenic locus notch homolog protein 1 (Q07008) · a predicted model of the same protein · chain D against A, TM-score 0.71

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 Q07008
• Every structure of UniProt D3ZHH1
• Elsewhere: RCSB PDB 4XL1 · PDBe 4XL1 · UniProt Q07008 · UniProt D3ZHH1