SMTL ID : 5npr.1

The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ACE- VAL- THR- PRO- VAL- CYS- THR- ALA- NH2: bisubstrate inhibitor(Non-covalent)

ACE-VAL-THR-PRO-VAL-CYS-THR-ALA-NH2.1: 13 residues within 4Å: Chain A: H.182, H.184, H.185, N.243, H.244, P.245, Y.318, T.319, K.320, Q.525, F.554, V.581 Ligands: 94T.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.320, A:F.554 Hydrogen bonds: A:Y.318, A:K.320 Water bridges: A:H.185, A:G.321, A:Q.525, A:Q.525, A:Q.525

1 x K: POTASSIUM ION(Non-functional Binders)

K.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x 94T: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] propyl hydrogen phosphate(Non-covalent)

94T.3: 21 residues within 4Å: Chain A: P.245, H.248, N.524, Q.525, K.528, L.552, F.554, V.581, A.582, K.584, H.587, R.590, G.605, H.606, T.607, T.608, D.611 Ligands: ACE-VAL-THR-PRO-VAL-CYS-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-CYS-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-CYS-THR-ALA-NH2.1, ACE-VAL-THR-PRO-VAL-CYS-THR-ALA-NH2.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.552, A:F.554 Hydrogen bonds: A:H.248, A:N.524, A:Q.525, A:A.582, A:A.582, A:K.584, A:H.587, A:R.590, A:H.606, A:T.607, A:T.608, A:T.608 Water bridges: A:Y.527, A:Y.527, A:K.584, A:K.584, A:H.587 Salt bridges: A:K.528, A:K.528 pi-Stacking: A:H.587

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rafie, K. et al., Thio-Linked UDP-Peptide Conjugates as O-GlcNAc Transferase Inhibitors. Bioconjug. Chem. (2018)

Release Date

2018-05-16

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit