Research workbench
Cryo-EM structure of the ternary complex between netrin-1, neogenin and repulsive guidance molecule B
Analyse Cryo-EM structure of the ternary complex between netrin-1, neogenin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NDG
- Type
- protein
- Length
- 2,643 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1; Neogenin; Repulsive guidance molecule B (C-terminal region); Rgm domain family…
- UniProt
- O95631, Q7TQG5, Q6NW40
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.67
Structure
electron microscopy · 4 distinct chains · 4% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, D | Netrin-1 | protein | 416 | 8% helix, 30% strand | O95631 |
| B, H, E | Neogenin | protein | 299 | 0% helix, 43% strand | Q7TQG5 |
| F, C, I | Repulsive guidance molecule B (C-terminal region) | protein | 151 | 3% helix, 44% strand | Q6NW40 |
| N, M, O | Rgm domain family member B | protein | 15 | 0% helix, 47% strand | Q6NW40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, G, H, D, E
- CA · Calcium ion · metal · 3 copies · chains A, G, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.67 | 0.79 | 51 | empty |
| 2 | 474 | 0.67 | 0.79 | 47 | empty |
| 3 | 371 | 0.65 | 0.80 | 42 | empty |
| 4 | 530 | 0.60 | 0.74 | 56 | empty |
| 5 | 494 | 0.59 | 0.74 | 57 | empty |
Interfaces
18 interfaces between chains.
- E–I · 1453 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1452 Ų buried · 24 hydrogen bonds · protein-protein
- C–H · 1448 Ų buried · 24 hydrogen bonds · protein-protein
- C–M · 1073 Ų buried · 16 hydrogen bonds · protein-protein
- F–N · 1072 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7NDG · Cryo-EM structure of the ternary complex between Netrin-1, Neogenin and Repulsive… · the same entry in another collection · chain O against O, TM-score 1.00
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 7NDG · PDBe 7NDG · UniProt O95631 · UniProt Q7TQG5 · UniProt Q6NW40
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