SMTL ID : 6q4m.1

Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 12V: (2S,3R,4R,5S,6R)-3-(acetylamino)-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-covalent)

12V.1: 24 residues within 4Å: Chain A: P.251, T.252, L.345, G.346, P.348, F.386, F.529, N.530, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, C.609, G.611, H.612, T.613, T.614, D.617 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.348, A:L.558, A:F.560 Hydrogen bonds: A:T.252, A:L.345, 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.613, A:T.614 Water bridges: A:Q.531, A:T.614, A:T.614 Salt bridges: A:K.534, A:K.534 pi-Stacking: A:H.593

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: P.128, I.131, V.158, V.563, N.567 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.567 PO4.3: 9 residues within 4Å: Chain A: S.487, T.492, I.495, N.496, A.499, P.506, R.507, T.508, I.510 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.487, A:T.492, A:R.507, A:T.508, A:T.508 Water bridges: A:N.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gundogdu, M. et al., Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation. To Be Published

Release Date

2019-12-25

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