GL1X · GenesisL1 explorer

Research workbench

Crystal structure of mouse nectin-2 extracellular fragment D1-D2

Analyse Crystal structure of mouse nectin-2 extracellular fragment D1-D2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4FMK
Type
protein
Length
221 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Poliovirus receptor-related protein 2
UniProt
P32507
Ligands
NAG, MAN, BMA, FUC, CD
Pockets
1 · best druggability 0.37

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 52% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APoliovirus receptor-related protein 2protein2213% helix, 52% strandP32507

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
  • MAN · alpha-D-mannopyranose · sugar · 3 copies
  • BMA · beta-D-mannopyranose · sugar · 2 copies
  • FUC · alpha-L-fucopyranose · sugar · 2 copies
  • CD · Cadmium ion · metal · 4 copies · chains A

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1730.370.7716empty

Modifications

Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

  • 4FMK · Crystal structure of mouse nectin-2 extracellular fragment D1-D2 · 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 0.94

Analyse

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.