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

Crystal structure of human O-GlcNAc transferase bound to substrate 7 and a peptide from HCF-1 pro-repeat 2 (11-26)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NJ5: [[(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] [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[6-(butanoylamino)hexanoylamino]-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate(Non-covalent)

NJ5.1: 35 residues within 4Å: Chain A: H.152, I.156, H.189, H.190, M.192, L.193, H.249, P.250, T.251, H.253, L.254, L.344, G.345, P.347, F.385, F.528, Q.530, Y.532, K.533, L.557, F.559, V.586, A.587, P.588, K.589, H.592, R.595, C.608, G.610, H.611, T.612, T.613, D.616, A.633 Ligands: NG8.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.347, A:Y.532, A:L.557, A:F.559 Hydrogen bonds: A:H.152, A:H.189, A:T.251, A:Q.530, A:Y.532, A:A.587, A:A.587, A:K.589, A:H.592, A:R.595, A:H.611, A:H.611, A:T.612, A:T.612, A:T.613 Water bridges: A:L.344, A:K.533, A:R.595, A:T.613 Salt bridges: A:K.533, A:H.611 pi-Stacking: A:H.592 NJ5.3: 35 residues within 4Å: Chain C: H.152, I.156, H.189, H.190, M.192, L.193, H.249, P.250, T.251, H.253, L.254, L.344, G.345, P.347, F.385, F.528, Q.530, Y.532, K.533, L.557, F.559, V.586, A.587, P.588, K.589, H.592, R.595, C.608, G.610, H.611, T.612, T.613, D.616, A.633 Ligands: NG8.4 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:P.347, C:Y.532, C:L.557, C:F.559 Hydrogen bonds: C:H.152, C:H.189, C:T.251, C:Q.530, C:Y.532, C:A.587, C:A.587, C:K.589, C:H.592, C:R.595, C:H.611, C:H.611, C:T.612, C:T.612, C:T.613 Water bridges: C:L.344, C:K.533, C:R.595, C:T.613 Salt bridges: C:K.533, C:H.611 pi-Stacking: C:H.592

2 x NG8: 3-[2,2-bis(fluoranyl)-10,12-dimethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-4,6,9,11-tetraen-4-yl]-~{N}-ethyl-propanamide(Non-covalent)

NG8.2: 18 residues within 4Å: Chain A: G.124, I.126, I.156, Q.530, L.531, Y.532, R.558, F.559, P.560, P.585, V.586 Chain C: K.66, L.86, D.91, Q.93, G.94, Q.97 Ligands: NJ5.1 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.126, A:I.156, A:Q.530, A:F.559, A:V.586, C:L.86, C:Q.93, C:Q.97 NG8.4: 18 residues within 4Å: Chain A: K.66, L.86, D.91, Q.93, G.94, Q.97 Chain C: G.124, I.126, I.156, Q.530, L.531, Y.532, R.558, F.559, P.560, P.585, V.586 Ligands: NJ5.3 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.86, A:Q.93, A:Q.97, C:I.126, C:I.156, C:Q.530, C:F.559, C:V.586

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alteen, M.G. et al., A Direct Fluorescent Activity Assay for Glycosyltransferases Enables Convenient High-Throughput Screening: Application to O-GlcNAc Transferase. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-03-04

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: AC
HCF-1 pro-repeat 2 (11-26): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
AAA

B
BBB

D
BBB

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

HCF-1 pro-repeat 2 (11-26)

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