SMTL ID : 8ui1.1

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 at pH 7.3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.91 Å

Oligo State

monomer

Ligands

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

UDP.1: 15 residues within 4Å: Chain A: V.114, F.115, Y.116, E.118, D.147, R.181, G.183, I.184, R.188, D.204, S.205, H.206, W.314, R.345 Ligands: MN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.184 Hydrogen bonds: A:V.114, A:Y.116, A:D.147, A:D.147, A:R.181, A:G.183, A:S.205, A:S.205 Water bridges: A:R.345, A:R.345 Salt bridges: A:H.206, A:R.345, A:R.345

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

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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 13 residues within 4Å: Chain A: L.255, H.261, E.264, H.266, Q.267, D.419, F.469, V.472, H.474, M.476, D.481, E.482, C.494 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.264, A:Q.267, A:H.474 GOL.4: 8 residues within 4Å: Chain A: D.374, W.377, R.378, P.548, F.551, T.552, F.553, P.554 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.378, A:T.552 GOL.5: 5 residues within 4Å: Chain A: T.285, W.326, W.409, N.413, V.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.285, A:T.285 GOL.6: 7 residues within 4Å: Chain A: T.505, S.507, Q.509, M.511, C.531, D.532, D.533 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.509, A:D.533 GOL.8: 5 residues within 4Å: Chain A: N.386, R.388, P.389, E.390, S.391 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.386, A:N.386, A:R.388, A:E.390

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

PEG.7: 7 residues within 4Å: Chain A: H.266, R.270, P.416, K.471, V.472, G.496, W.501 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.270, A:R.270, A:K.471

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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