MolNFT v1 · #183072 · protein
Structure of the complex between netrin-1 and its receptor neogenin
7NE1: “Structure of the complex between netrin-1 and its receptor neogenin”. X-ray diffraction, 5 ligands (GU4, YYJ, NAG), 6 pockets (best druggability 0.64). MolNFT v1 #183072 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NE1
- Type
- protein
- Length
- 719 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1; Neogenin
- UniProt
- O95631, Q7TQG5
- Ligands
- GU4, YYJ, NAG, CA, NO3
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-1 | protein | 414 | 9% helix, 31% strand | O95631 |
| B | Neogenin | protein | 305 | 1% helix, 46% strand | Q7TQG5 |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains A
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · chains A
- NO3 · Nitrate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.64 | 0.79 | 34 | empty |
| 2 | 153 | 0.61 | 0.84 | 31 | empty |
| 3 | 94 | 0.51 | 0.82 | 25 | empty |
| 4 | 169 | 0.44 | 0.74 | 26 | NO3 |
| 5 | 103 | 0.41 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 744 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 4 glycan (disulfide, N-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 O95631
- Every structure of UniProt Q7TQG5
- Elsewhere: RCSB PDB 7NE1 · PDBe 7NE1 · UniProt O95631 · UniProt Q7TQG5
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