SMTL ID : 6e37.2 (1 other biounit)

O-GlcNAc Transferase in complex with covalent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-2-2-mer

Ligands

2 x HQV: (2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)(Covalent)

HQV.1: 33 residues within 4Å: Chain A: H.190, M.193, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, P.589, K.590, H.593, R.596, C.609, N.610, G.611, H.612, T.613, T.614, D.617 Chain B: T.6, P.7, V.8, S.9 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.558 Hydrogen bonds: A:T.252, A:A.588, A:A.588, A:K.590, A:H.593, A:R.596, A:H.612, A:H.612, A:T.613, A:T.614, B:S.9, B:S.9 Water bridges: A:H.254, A:L.345, A:Q.531, A:Y.533, A:K.534 Salt bridges: A:K.534, A:K.534, A:H.612 pi-Stacking: A:H.593 HQV.2: 33 residues within 4Å: Chain C: H.190, M.193, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, P.589, K.590, H.593, R.596, C.609, N.610, G.611, H.612, T.613, T.614, D.617 Chain D: T.6, P.7, V.8, S.9 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.558 Hydrogen bonds: C:T.252, C:A.588, C:A.588, C:K.590, C:R.596, C:H.612, C:H.612, C:T.613, C:T.613, C:T.614, D:S.9, D:S.9 Water bridges: C:L.345, C:Q.531, C:K.534 Salt bridges: C:K.534, C:K.534, C:H.612 pi-Stacking: C:H.593

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Worth, M. et al., Targeted covalent inhibition of O-GlcNAc transferase in cells. Chem.Commun.(Camb.) (2019)

Release Date

2019-11-06

Peptides

O-GlcNAc transferase subunit p110: AC
TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

O-GlcNAc transferase subunit p110

TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN

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