SMTL ID : 4xi9.2 (3 other biounits)

Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x VAL- THR- PRO- VAL- SER- THR- ALA- ALA: Retinoblastoma-like protein 2(Non-covalent)

VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1: 14 residues within 4Å: Chain A: H.188, H.190, H.191, N.249, H.250, P.251, Y.324, T.325, K.326, Q.531, F.560, V.587, A.588 Ligands: 12V.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.560 Hydrogen bonds: A:Y.324, A:K.326

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.2: 28 residues within 4Å: Chain A: H.190, H.250, P.251, T.252, H.254, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, F.560, V.587, A.588, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 Ligands: VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1, VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1, VAL-THR-PRO-VAL-SER-THR-ALA-ALA.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.558, A:F.560 Hydrogen bonds: A:T.252, A:T.252, A:Q.531, A:Y.533, A:A.588, A:A.588, A:K.590, A:H.593, A:R.596, A:H.612, A:H.612, A:H.612, A:T.613, A:T.613, A:T.614 Salt bridges: A:K.534, A:K.534 pi-Stacking: A:H.593

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pathak, S. et al., The active site of O-GlcNAc transferase imposes constraints on substrate sequence. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-08-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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