MolNFT v1 · #114098 · protein
Dimer structure of murine nectin-3 D1D2
5B22: “Dimer structure of murine nectin-3 D1D2”. X-ray diffraction, 2 ligands (NAG, BMA), 1 pocket (best druggability 0.25). MolNFT v1 #114098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B22
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nectin-3
- UniProt
- Q9JLB9
- Ligands
- NAG, BMA
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nectin-3 | protein | 209 | 4% helix, 56% strand | Q9JLB9 |
| B | Nectin-3 | protein | 211 | 3% helix, 58% strand | Q9JLB9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.25 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 791 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 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 Q9JLB9
- Elsewhere: RCSB PDB 5B22 · PDBe 5B22 · UniProt Q9JLB9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.