GL1X · GenesisL1 explorer

Research workbench

Deglycosylated nogo receptor with native disulfide structure

Analyse Deglycosylated nogo receptor with native disulfide structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5O0R
Type
protein
Length
573 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Reticulon-4 receptor
UniProt
Q99PI8
Ligands
NAG, CL
Pockets
1 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AReticulon-4 receptorprotein2898% helix, 17% strandQ99PI8
BReticulon-4 receptorprotein2848% helix, 18% strandQ99PI8

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
  • CL · Chloride ion · ion · 3 copies · chains A, B
  • GOL · Glycerol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
18320.750.7980CL

Interfaces

1 interface between chains.

  • A–B · 396 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

  • 5O0R · Deglycosylated Nogo Receptor with native disulfide structure · the same entry in another collection · chain A against A, TM-score 1.00
  • Q99PI8 · AlphaFold monomer V2.0 prediction for reticulon-4 receptor (Q99PI8) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

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