GL1X · GenesisL1 explorer

Research workbench

Extracellular domain of the LDL receptor

Analyse Extracellular domain of the LDL receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1N7D
Type
protein
Length
639 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Low-density lipoprotein receptor
UniProt
P01130
Ligands
KEG, NAG, MAN, BMA, CA
Pockets
9 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ALow-density lipoprotein receptorprotein6390% helix, 14% strandP01130

Ligands and binding sites

  • KEG · 12-tungstophosphate · ligand · 3 copies · chains A
  • 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
  • CA · Calcium ion · metal · 8 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11450.760.9334empty
24610.750.8470empty
39710.730.7690empty
42630.600.7944empty
5910.570.8626empty

Modifications

Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

  • 1N7D · Extracellular domain of the LDL receptor · the same entry in another collection · chain A against A, TM-score 1.00
  • P01130 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor (P01130) · a predicted model of the same protein · chain A against A, TM-score 0.68

Analyse

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