MolNFT v1 · #91765 · protein
Crystal structure of mouse nectin-2 extracellular fragment D1-D2, 2ND crystal form
4FN0 · Poliovirus receptor-related protein 2: “Crystal structure of mouse nectin-2 extracellular fragment D1-D2, 2ND crystal form”. X-ray diffraction, 3 ligands (NAG, BMA, FUC), 3 pockets (best druggability 0.55). MolNFT v1 #91765 on…
- PDB
- 4FN0
- Type
- protein
- Length
- 659 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poliovirus receptor-related protein 2
- UniProt
- P32507
- Ligands
- NAG, BMA, FUC
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Poliovirus receptor-related protein 2 | protein | 220 | 3% helix, 52% strand | P32507 |
| C | Poliovirus receptor-related protein 2 | protein | 219 | 4% helix, 53% strand | P32507 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.55 | 0.86 | 16 | empty |
| 2 | 63 | 0.46 | 0.83 | 13 | empty |
| 3 | 73 | 0.35 | 0.77 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 814 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 681 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4FN0 · Crystal structure of mouse nectin-2 extracellular fragment D1-D2, 2nd crystal form · the same entry in another collection · chain A against A, TM-score 1.00
- P32507 · AlphaFold monomer V2.0 prediction for nectin-2 (P32507) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P32507
- Elsewhere: RCSB PDB 4FN0 · PDBe 4FN0 · UniProt P32507
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