MolNFT v1 · #181325 · protein
Netrin-1 in complex with sos
7LRF: “Netrin-1 in complex with sos”. X-ray diffraction, 7 ligands (GU4, YYJ, NAG), 9 pockets (best druggability 0.54). MolNFT v1 #181325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7LRF
- Type
- protein
- Length
- 829 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Netrin-1
- UniProt
- Q90922
- Ligands
- GU4, YYJ, NAG, BMA, CA, NA, CL
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Netrin-1 | protein | 418 | 6% helix, 31% strand | Q90922 |
| B | Netrin-1 | protein | 411 | 7% helix, 30% strand | Q90922 |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.54 | 0.77 | 41 | NA |
| 2 | 232 | 0.51 | 0.76 | 35 | PEG |
| 3 | 117 | 0.47 | 0.79 | 26 | empty |
| 4 | 94 | 0.40 | 0.77 | 18 | empty |
| 5 | 67 | 0.38 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1095 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 8 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 Q90922
- Elsewhere: RCSB PDB 7LRF · PDBe 7LRF · UniProt Q90922
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.