Research workbench
Complex of NOTCH1 (EGF11-13) bound to delta-like 4 (N-EGF2)
Analyse Complex of NOTCH1 (EGF11-13) bound to delta-like 4 (N-EGF2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XLW
- Type
- protein
- Length
- 1,496 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurogenic locus notch homolog protein 1; Delta-like protein
- UniProt
- Q07008, D3ZHH1
- Ligands
- BGC, NAG, FUC, CA
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 1% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neurogenic locus notch homolog protein 1 | protein | 113 | 3% helix, 29% strand | Q07008 |
| B, F | Delta-like protein | protein | 257 | 0% helix, 41% strand | D3ZHH1 |
| C | Neurogenic locus notch homolog protein 1 | protein | 118 | 3% helix, 29% strand | Q07008 |
| D | Delta-like protein | protein | 258 | 0% helix, 41% strand | D3ZHH1 |
| E, G | Neurogenic locus notch homolog protein 1 | protein | 117 | 3% helix, 33% strand | Q07008 |
| H | Delta-like protein | protein | 259 | 0% helix, 42% strand | D3ZHH1 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 12 copies · chains A, B, E, C, D, G, F, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, F, D, H, A, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.67 | 0.90 | 24 | empty |
| 2 | 141 | 0.67 | 0.88 | 26 | empty |
| 3 | 139 | 0.65 | 0.87 | 25 | empty |
| 4 | 419 | 0.63 | 0.77 | 54 | FUC |
| 5 | 391 | 0.61 | 0.77 | 55 | FUC |
Interfaces
10 interfaces between chains.
- D–H · 1370 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 1336 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1072 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1061 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1057 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 disulfide, 24 glycan, 20 modified (disulfide, methylation, O-glycosylation, N-glycosylation, 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 Q07008
- Every structure of UniProt D3ZHH1
- Elsewhere: RCSB PDB 4XLW · PDBe 4XLW · UniProt Q07008 · UniProt D3ZHH1
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