SMTL ID : 8ujf.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 2.87 Å

Oligo State

hetero-2-1-mer

Ligands

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

UDP.1: 17 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 Ligands: MN.2 16 PLIP interactions: 16 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:D.204, A:S.205, A:S.205, A:W.314, A:R.345 Salt bridges: A:H.206, A:H.342, A:R.345 UDP.4: 19 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, Y.351 Ligands: MN.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.184 Hydrogen bonds: B:V.114, B:Y.116, B:Y.116, B:D.147, B:R.181, B:R.181, B:G.183, B:S.205, B:S.205, B:W.314, B:Y.351 Salt bridges: B:H.206, B:H.342, B:R.345, B:R.345 pi-Stacking: B:Y.351

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

MN.2: 4 residues within 4Å: Chain A: D.204, H.206, H.342 Ligands: UDP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.204, A:H.206, A:H.342 MN.3: 3 residues within 4Å: Chain A: H.261, E.264, R.495 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 MN.6: 4 residues within 4Å: Chain B: D.204, H.206, H.342 Ligands: UDP.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.204, B:H.206, B:H.342, H2O.1 MN.7: 2 residues within 4Å: Chain B: H.261, E.264 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.261, B:E.264, B:E.264, H2O.1, H2O.1

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.5: 12 residues within 4Å: Chain B: L.252, L.255, K.257, M.259, E.260, H.261, S.262, E.482, W.493 Chain C: P.4, S.5, P.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.257, B:E.260, B:H.261, B:S.262, B:E.482, B:E.482

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
Mucin-5AC: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Glycosyl transferase

Mucin-5AC

Related Entries With Identical Sequence