SMTL ID : 8uhz.1

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: D.146, G.148, S.149, R.155, E.156, R.177, N.178, E.179 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.156, A:E.156, A:R.177 GOL.2: 6 residues within 4Å: Chain A: R.177, N.178, E.179, V.180, K.182, K.190 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.177, A:N.178, A:E.179, A:V.180, A:V.180, A:K.182, A:K.190 GOL.3: 12 residues within 4Å: Chain A: L.255, H.261, E.264, H.266, Q.267, D.419, H.474, D.481, E.482, C.494, R.495 Ligands: MN.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.267, A:D.419, A:C.494 Water bridges: A:R.495 GOL.4: 8 residues within 4Å: Chain A: V.114, F.115, Y.116, D.147, R.181, G.183, I.184, W.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.116, A:D.147, A:R.181, A:R.181 GOL.6: 7 residues within 4Å: Chain A: H.266, A.269, R.270, K.471, V.472, G.496, W.501 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.266, A:R.270, A:R.270, A:K.471, A:G.496 GOL.7: 5 residues within 4Å: Chain A: S.225, N.297, A.299, F.300, D.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.225, A:S.225 GOL.8: 4 residues within 4Å: Chain A: R.86, P.89, K.242, H.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.86, A:K.242, A:H.243, A:H.243 GOL.9: 11 residues within 4Å: Chain A: K.251, Y.263, L.271, P.272, E.275, T.285, N.413, V.414, P.416, E.417 Ligands: PEG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.413, A:E.417, A:E.417 GOL.10: 7 residues within 4Å: Chain A: P.107, P.198, I.199, I.221, K.222, S.225, N.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.221, A:N.297

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

PEG.5: 5 residues within 4Å: Chain A: W.326, W.409, N.413, V.414 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.409 PEG.11: 7 residues within 4Å: Chain A: T.505, S.506, S.507, Q.509, C.531, D.532, D.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.507, A:Q.509, A:C.531

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

MN.12: 3 residues within 4Å: Chain A: D.204, H.206, H.342 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.206, A:H.342, H2O.1, H2O.1, H2O.2 MN.13: 4 residues within 4Å: Chain A: H.261, E.264, R.495 Ligands: GOL.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.261, A:E.264, A:E.264, H2O.2, H2O.3 MN.14: 4 residues within 4Å: Chain A: W.446, P.449, H.451, L.491 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.451, H2O.3, H2O.4, H2O.4, H2O.5

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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