SMTL ID : 5hgv.1 (3 other biounits)

Structure of an O-GlcNAc transferase point mutant, D554N in complex with peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 20 residues within 4Å: Chain A: P.247, Q.527, K.530, L.554, F.556, V.583, A.584, K.586, H.589, R.592, G.607, H.608, T.609, T.610, D.613 Chain B: T.6, P.7, V.8, S.9 Ligands: NAG.3 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.554, A:F.556 Hydrogen bonds: A:H.250, A:N.526, A:Q.527, A:A.584, A:A.584, A:K.586, A:H.589, A:R.592, A:H.608, A:T.609, A:T.610, A:T.610, B:S.9 Water bridges: A:Y.529, A:H.589 Salt bridges: A:K.530, A:K.530 pi-Stacking: A:H.589

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: G.53, K.54, L.55, Q.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.53, A:L.55, A:Q.56, A:Q.56 SO4.4: 5 residues within 4Å: Chain A: K.322, G.323, A.324 Chain B: N.12, M.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.323, A:A.324, B:M.13 Salt bridges: A:K.322 Water bridges: B:N.12

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 14 residues within 4Å: Chain A: H.186, M.189, P.247, T.248, L.251, L.341, G.342, P.344, F.382, Y.529, H.608, T.609 Chain B: S.9 Ligands: UDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.248, A:L.341, A:H.608

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Janetzko, J. et al., How the glycosyltransferase OGT catalyzes amide bond cleavage. Nat.Chem.Biol. (2016)

Release Date

2016-09-14

Peptides

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit: A
TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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

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