SMTL ID : 6fsn.1

Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-glucose (conformation 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.19 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: H.42, T.43, N.44, D.127 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.44

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.119, D.121, D.252, L.253, K.263 Ligands: UPG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.119, A:D.121, A:D.121, A:D.252, H2O.1

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

UPG.3: 22 residues within 4Å: Chain A: A.23, S.24, G.25, Y.28, Q.93, W.97, K.100, F.117, D.119, D.121, I.175, S.176, A.177, N.211, D.213, Q.214, D.252, L.253, C.254, N.255, K.263 Ligands: CA.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:Y.28, A:W.97, A:K.100, A:D.119, A:S.176, A:D.213, A:L.253, A:N.255 Water bridges: A:K.263, A:K.263 Salt bridges: A:K.263, A:K.263 pi-Stacking: A:Y.28

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: L.136, D.137, A.139, P.225, I.226, A.227, T.228 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.137, A:I.226 Water bridges: A:I.226, A:T.228

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 4 residues within 4Å: Chain A: E.53, Q.54, K.61, T.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61 Water bridges: A:E.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caputo, A.T. et al., Crystal polymorphism in fragment-based lead discovery of ligands of the catalytic domain of UGGT, the glycoprotein folding quality control checkpoint. Front Mol Biosci (2022)

Release Date

2019-03-20

Peptides

UDP-glucose-glycoprotein glucosyltransferase-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-glucose-glycoprotein glucosyltransferase-like protein

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