Galnac-T2 crystal soaked with udp-5SGALNAC, MEA2 and manganese (higher resolution dataset)

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).

Ligands and binding sites

• HWU · (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 6 copies · chains A, B, X, C, D, E, Y, F
• BBK · 2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose · ligand · 4 copies · chains A, D, B, E
• MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
• EDO · 1,2-ethanediol · additive · 37 copies · chains A, E, B, D, X, Y, C

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Interfaces

13 interfaces between chains.

• C–F · 1700 Ų buried · 9 hydrogen bonds · protein-protein
• A–D · 1654 Ų buried · 15 hydrogen bonds · protein-protein
• B–E · 1554 Ų buried · 12 hydrogen bonds · protein-protein
• A–E · 582 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 568 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide (disulfide).

Compared structures

• 4D0Z · GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset) · the same entry in another collection · chain Y against Y, TM-score 1.00
• Q10471 · AlphaFold monomer V2.0 prediction for polypeptide N-acetylgalactosaminyltransferase 2… · a predicted model of the same protein · chain B against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q10471
• Elsewhere: RCSB PDB 4D0Z · PDBe 4D0Z · UniProt Q10471