SMTL ID : 4gz6.3 (4 other biounits)

Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.98 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: 25 residues within 4Å: Chain A: H.190, M.193, P.251, T.252, L.255, L.345, G.346, P.348, F.386, F.529, Q.531, Y.533, K.534, L.558, V.587, A.588, P.589, K.590, H.593, R.596, C.609, H.612, T.613, T.614, D.617 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.558 Hydrogen bonds: A:T.252, A:L.345, A:Q.531, A:A.588, A:A.588, A:K.590, A:K.590, A:H.593, A:H.593, A:R.596, A:H.612, A:H.612, A:H.612, A:T.613, A:T.613, A:T.614, A:T.614 Salt bridges: A:K.534, A:K.534 pi-Stacking: A:H.593

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

SO4.2: 4 residues within 4Å: Chain A: N.13, N.17, A.44, N.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:N.17, A:N.48 SO4.3: 3 residues within 4Å: Chain A: R.559, F.584, P.586 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.559 Salt bridges: A:R.559 SO4.4: 3 residues within 4Å: Chain A: M.628, N.654, R.655 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.654, A:R.655 Salt bridges: A:R.655 SO4.5: 5 residues within 4Å: Chain A: G.57, K.58, L.59, Q.60, E.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.57, A:L.59, A:Q.60, A:E.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lazarus, M.B. et al., Structural snapshots of the reaction coordinate for O-GlcNAc transferase. Nat.Chem.Biol. (2012)

Release Date

2012-10-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

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

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