SMTL ID : 5ndf.1 (4 other biounits)

Small-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.224, H.226, H.359 Ligands: UDP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.224, A:H.226, A:H.359, H2O.2 MN.4: 4 residues within 4Å: Chain B: D.224, H.226, H.359 Ligands: UDP.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.224, B:H.226, B:H.359, H2O.7

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.2: 17 residues within 4Å: Chain A: T.143, F.144, H.145, D.176, R.201, G.203, L.204, D.224, S.225, H.226, V.330, W.331, H.359, R.362, Y.367 Ligands: MN.1, EDO.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.143, A:H.145, A:D.176, A:D.176, A:R.201, A:G.203, A:S.225, A:S.225, A:S.225, A:W.331, A:Y.367 Water bridges: A:H.145, A:R.362, A:R.362, A:R.362 Salt bridges: A:H.226, A:H.359, A:R.362 pi-Stacking: A:Y.367 UDP.5: 16 residues within 4Å: Chain B: T.143, F.144, H.145, D.176, R.201, G.203, L.204, D.224, S.225, H.226, V.330, W.331, H.359, R.362, Y.367 Ligands: MN.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.145, B:H.145, B:D.176, B:R.201, B:S.225, B:S.225, B:S.225, B:H.365 Water bridges: B:R.362, B:R.362 Salt bridges: B:H.226, B:H.359, B:R.362 pi-Stacking: B:Y.367

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: A.307, G.308, G.309, W.331, G.332, E.334 Ligands: UDP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.332 Water bridges: A:A.307, A:G.309 EDO.6: 5 residues within 4Å: Chain B: N.198, D.199, R.200, E.202, R.210 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.198, B:D.199, B:D.199, B:D.199, B:R.200, B:E.202, B:E.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., The small molecule luteolin inhibits N-acetyl-alpha-galactosaminyltransferases and reduces mucin-type O-glycosylation of amyloid precursor protein. J. Biol. Chem. (2017)

Release Date

2017-11-01

Peptides

Polypeptide N-acetylgalactosaminyltransferase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
C

Polypeptide N-acetylgalactosaminyltransferase 2

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