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Blood group synthase aaglyb in complex with ump and cryoprotected with glycerol

Analyse Blood group synthase aaglyb in complex with ump and cryoprotected with glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5M79
Type
protein
Length
293 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Histo-blood group abo system transferase
EC
2.4.1.40, 2.4.1.37
UniProt
P16442
Ligands
U5P, MN, SO4
Pockets
1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHisto-blood group abo system transferase (EC 2.4.1.40, 2.4.1.37)protein29335% helix, 19% strandP16442

Ligands and binding sites

  • U5P · Uridine-5'-monophosphate · ligand · chains A
  • MN · Manganese (II) ion · metal · chains A
  • SO4 · Sulfate ion · ion · 2 copies · chains A
  • GOL · Glycerol · additive · 3 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
14350.740.8341MN, U5P, GOL

Compared structures

  • 5M79 · Blood group synthase AAGlyB in complex with UMP and cryoprotected with glycerol · the same entry in another collection · chain A against A, TM-score 1.00
  • P16442 · AlphaFold monomer V2.0 prediction for histo-blood group abo system transferase (P16442) · a predicted model of the same protein · chain A against A, TM-score 1.00

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