SMTL ID : 8uje.1

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and Muc5AC-3,13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

UDP.1: 18 residues within 4Å: Chain A: V.114, F.115, Y.116, E.118, D.147, R.181, G.183, I.184, A.187, R.188, D.204, S.205, H.206, W.314, H.342, R.345, Y.351 Ligands: MN.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.116, A:E.118, A:E.118, A:D.147, A:D.147, A:R.181, A:R.181, A:G.183, A:S.205, A:S.205, A:W.314, A:Y.351 Water bridges: A:R.345, A:R.345 Salt bridges: A:H.206, A:H.342, A:R.345 pi-Stacking: A:Y.351

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

MN.2: 4 residues within 4Å: Chain A: D.204, H.206, H.342 Ligands: UDP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:H.206, A:H.342, H2O.1 MN.3: 3 residues within 4Å: Chain A: H.261, E.264, R.495 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.261, A:E.264, H2O.1, H2O.1, H2O.1

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 7 residues within 4Å: Chain A: P.89, D.90, A.91, H.243, I.244, A.245, Y.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.341 PEG.5: 5 residues within 4Å: Chain A: S.406, R.408, W.409, E.412, N.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.406, A:W.409, A:N.413 PEG.6: 6 residues within 4Å: Chain A: K.251, T.285, W.326, W.409, N.413, V.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.285, A:N.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, P. et al., A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is distinct from host homologues. Nat Commun (2024)

Release Date

2024-05-15

Peptides

Glycosyl transferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycosyl transferase

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