SMTL ID : 7zxw.1

Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with the 5-[(morpholin-4-yl)methyl]quinolin-8-ol inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 3 residues within 4Å: Chain A: H.38, T.39, N.40 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.115, D.117, D.248 Ligands: UPG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.115, A:D.117, A:D.117, A:D.248, H2O.1

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

UPG.3: 19 residues within 4Å: Chain A: A.19, S.20, Y.24, Q.89, W.93, K.96, D.115, D.117, S.172, A.173, N.207, D.209, D.248, L.249, C.250, N.251, K.259 Ligands: CA.2, DMS.6 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.20, A:S.20, A:Y.24, A:K.96, A:K.96, A:D.115, A:N.207, A:L.249, A:N.251 Water bridges: A:S.20, A:Q.89, A:K.259, A:K.259 Salt bridges: A:K.259, A:K.259 pi-Stacking: A:Y.24

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: Q.89, W.93, N.251 Ligands: UPG.3 No protein-ligand interaction detected (PLIP) DMS.7: 2 residues within 4Å: Chain A: R.264, R.265 No protein-ligand interaction detected (PLIP) DMS.8: 3 residues within 4Å: Chain A: H.38, R.121, E.269 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.269 DMS.9: 4 residues within 4Å: Chain A: Y.76, P.79, W.81, R.192 No protein-ligand interaction detected (PLIP)

1 x JM3: 5-(morpholin-4-ylmethyl)quinolin-8-ol(Non-covalent)

JM3.5: 10 residues within 4Å: Chain A: F.154, Y.159, W.160, Y.163, S.204, L.205, A.206, N.207, D.211, H.215 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.159 Hydrogen bonds: A:A.206, A:N.207, A:H.215 Salt bridges: A:D.211 pi-Stacking: A:W.160, A:W.160

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

2022-11-30

Peptides

UDP-glucose-glycoprotein glucosyltransferase-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-glucose-glycoprotein glucosyltransferase-like protein