SMTL ID : 5hgv.4 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

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

UDP.1: 21 residues within 4Å: Chain A: P.247, N.526, 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.2 21 PLIP interactions: 19 interactions with chain A, 2 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, B:S.9 Water bridges: A:Y.529, A:T.610, A:T.610, B:S.9 Salt bridges: A:K.530, A:K.530 pi-Stacking: A:H.589 UDP.4: 21 residues within 4Å: Chain C: P.247, N.526, 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 D: T.6, P.7, V.8, S.9 Ligands: NAG.5 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.554, C:F.556 Hydrogen bonds: C:N.526, C:Q.527, C:A.584, C:A.584, C:K.586, C:H.589, C:H.589, C:R.592, C:H.608, C:T.609, C:T.609, C:T.610, C:T.610, D:S.9 Salt bridges: C:K.530, C:K.530 pi-Stacking: C:H.589 Water bridges: D:S.9

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

NAG.2: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.248, A:H.608 Water bridges: A:T.248, A:T.248, A:L.341 NAG.5: 14 residues within 4Å: Chain C: 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 D: S.9 Ligands: UDP.4 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.248, C:H.608 Water bridges: C:L.341

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

SO4.3: 5 residues within 4Å: Chain A: K.322, G.323, A.324 Chain B: N.12, M.13 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.13, A:G.323, A:A.324 Salt bridges: A:K.322 SO4.6: 5 residues within 4Å: Chain C: K.322, G.323, A.324 Chain D: N.12, M.13 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.323, C:A.324, D:M.13 Salt bridges: C:K.322

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: AC
TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN-MET-MET: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
C

B
D

D
D

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

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

Related Entries With Identical Sequence