MolNFT v1 · #183071 · protein
Structure of the ternary complex between netrin-1, repulsive-guidance molecule-B (rgmb) and neogenin
7NE0: “Structure of the ternary complex between netrin-1, repulsive-guidance molecule-B (rgmb) and neogenin”. X-ray diffraction, 5 ligands (GU4, YYJ, NAG), 9 pockets (best druggability 0.67). MolNFT v1 #183071 on GenesisL1: 3D structure…
- PDB
- 7NE0
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1; Neogenin; Repulsive guidance molecule B; Repulsive guidance molecule B…
- UniProt
- O95631, Q7TQG5, Q6NW40
- Ligands
- GU4, YYJ, NAG, CA, SO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-1 | protein | 416 | 8% helix, 31% strand | O95631 |
| B | Neogenin | protein | 299 | 0% helix, 42% strand | Q7TQG5 |
| C | Repulsive guidance molecule B | protein | 15 | 0% helix, 47% strand | Q6NW40 |
| D | Repulsive guidance molecule B C-terminal region (chain D) | protein | 161 | 6% helix, 41% strand | Q6NW40 |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · 4 copies · chains A, B, D
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.67 | 0.79 | 48 | empty |
| 2 | 148 | 0.54 | 0.81 | 20 | empty |
| 3 | 160 | 0.52 | 0.79 | 27 | empty |
| 4 | 155 | 0.52 | 0.79 | 23 | empty |
| 5 | 97 | 0.50 | 0.82 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1448 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1144 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 342 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7NE0 · Structure of the ternary complex between Netrin-1, Repulsive-Guidance Molecule-B (RGMB)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NW40 · AlphaFold monomer V2.0 prediction for rgm domain family member B (Q6NW40) · a predicted model of the same protein · chain D against A, TM-score 0.94
- O95631 · AlphaFold monomer V2.0 prediction for netrin-1 (O95631) · a predicted model of the same protein · chain A against A, TM-score 0.93
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
- Every structure of UniProt Q6NW40
- Elsewhere: RCSB PDB 7NE0 · PDBe 7NE0 · UniProt O95631 · UniProt Q7TQG5 · UniProt Q6NW40
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.