SMTL ID : 8ujh.1

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and a CST1 diglycopeptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

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

UDP.1: 22 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, F.313, W.314, H.342, R.345, Y.351 Chain B: T.1, T.2, T.3 Ligands: MN.3 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.184 Hydrogen bonds: A:Y.116, A:E.118, A:D.147, A:D.147, A:R.181, A:R.181, A:G.183, A:S.205, A:W.314, A:Y.351, B:T.3, B:T.3 Salt bridges: A:H.206, A:H.206, A:H.342, A:R.345 pi-Stacking: A:Y.351

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: W.493, R.495 Ligands: NGA.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.495

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

MN.3: 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.4: 3 residues within 4Å: Chain A: L.255, H.261, E.264 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.261, A:E.264, A:E.264, H2O.1, H2O.1

1 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.5: 15 residues within 4Å: Chain A: I.248, L.252, L.255, K.257, M.259, E.260, H.261, S.262, E.482, W.493 Chain B: T.3, T.4, K.6, P.7 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.260 Hydrogen bonds: A:E.260, A:H.261, A:S.262

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
SAG-related sequence SRS44: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Glycosyl transferase

SAG-related sequence SRS44

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