SMTL ID : 8ujg.1

X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

hetero-2-1-mer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.204, H.206, H.342 Ligands: UDP.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.204, A:H.206, A:H.342, H2O.4 MN.2: 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.3, H2O.5, H2O.5 MN.10: 4 residues within 4Å: Chain B: D.204, H.206, H.342 Ligands: UDP.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.204, B:D.204, B:H.206, B:H.342, H2O.5 MN.11: 3 residues within 4Å: Chain B: H.261, E.264, R.495 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.261, B:E.264, H2O.6, H2O.6, H2O.9

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

UDP.3: 19 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 Ligands: MN.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.184, A:Y.351 Hydrogen bonds: A:Y.116, A:E.118, A:E.118, A:D.147, A:D.147, A:R.181, A:R.181, A:S.205, A:S.205, A:W.314, A:Y.351 Water bridges: A:R.345, A:R.345, A:R.345, A:R.345, A:R.345 Salt bridges: A:H.206, A:H.342, A:R.345 UDP.12: 18 residues within 4Å: Chain B: 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 Ligands: MN.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:V.114, B:Y.116, B:D.147, B:R.181, B:R.181, B:S.205 Water bridges: B:Y.116, B:R.345, B:R.345, B:R.345 Salt bridges: B:H.206, B:H.342, B:R.345

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: L.76, Y.77, D.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.76 GOL.5: 6 residues within 4Å: Chain A: R.86, T.87, A.88, P.89, K.242, H.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.87, A:H.243, A:H.243 GOL.6: 5 residues within 4Å: Chain A: N.386, R.388, P.389, E.390, S.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.390, A:S.391 GOL.8: 12 residues within 4Å: Chain A: Q.327, C.328, G.329, K.402, G.403, C.404, K.405 Chain B: D.356, T.359, P.383, R.384, V.385 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.328, A:G.403, A:K.405 GOL.13: 7 residues within 4Å: Chain B: D.374, W.377, R.378, P.548, F.551, T.552, P.554 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.374, B:D.374, B:T.552 GOL.14: 7 residues within 4Å: Chain B: P.89, D.90, A.91, H.243, I.244, A.245, Y.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.243 Water bridges: B:A.245 GOL.15: 3 residues within 4Å: Chain B: L.76, Y.77, D.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.76, B:D.80 GOL.16: 5 residues within 4Å: Chain B: D.310, R.388, P.389, E.390, S.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.390 GOL.17: 7 residues within 4Å: Chain B: T.505, S.507, Q.509, M.511, C.531, D.532, D.533 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.509, B:Q.509, B:D.532, B:D.532, B:D.533 GOL.19: 5 residues within 4Å: Chain B: S.406, R.408, W.409, E.412, N.413 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.406, B:E.412, B:E.412 Water bridges: B:S.406

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

PEG.7: 6 residues within 4Å: Chain A: H.266, R.270, K.471, V.472, G.496, W.501 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.270, A:R.270, A:G.496 Water bridges: A:R.270 PEG.18: 5 residues within 4Å: Chain B: H.266, R.270, K.471, V.472, W.501 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.270, B:R.270 Water bridges: B:R.270

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.9: 12 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 C: T.5, V.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.252 Hydrogen bonds: A:H.261, A:S.262, C:T.5, C:V.6

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: AB
SAG-related sequence SRS13: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Glycosyl transferase

SAG-related sequence SRS13

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