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MolNFT v1 · #114927 · protein

Crystal structure of gtb + udp-glc + di

5C4D · Histo-blood group abo system transferase: “Crystal structure of gtb + udp-glc + di”. X-ray diffraction, 3 ligands (DA8, UPG, MN), 3 pockets (best druggability 0.56). MolNFT v1 #114927 on GenesisL1: 3D structure, binding sites and…

PDB
5C4D
Type
protein
Length
279 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
DA8, UPG, MN
Pockets
3 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHisto-blood group abo system transferase (EC 2.4.1.40, 2.4.1.37)protein27933% helix, 20% strandP16442

Ligands and binding sites

  • DA8 · octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside · ligand · chains A
  • UPG · Uridine-5'-diphosphate-glucose · ligand · chains A
  • MN · Manganese (II) ion · metal · chains A
  • PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13020.560.7630MN, DA8, UPG
2550.330.7716empty
3580.290.7414empty

Compared structures

  • 5C4D · Crystal structure of GTB + UDP-Glc + DI · 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 0.99

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