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

Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc and a peptide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-2-2-mer

Ligands

2 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: 29 residues within 4Å: Chain A: H.190, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, 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 Chain B: T.6, P.7, V.8, S.9 27 PLIP interactions: 26 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.558, A:F.560 Hydrogen bonds: A:T.252, A:T.252, A:H.254, A:L.345, 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.614, B:S.9 Water bridges: A:Q.531, A:Y.533, A:K.590, A:T.614, A:T.614 Salt bridges: A:K.534, A:K.534 pi-Stacking: A:H.593 12V.3: 29 residues within 4Å: Chain C: H.190, H.250, P.251, T.252, L.255, L.345, G.346, P.348, F.386, 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 Chain D: T.6, P.7, V.8, S.9 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.558, C:F.560 Hydrogen bonds: C:T.252, C:L.345, C:Q.531, C:A.588, C:A.588, C:K.590, C:H.593, C:H.593, C:R.596, C:H.612, C:H.612, C:T.613, C:T.613, C:T.614, C:T.614, D:S.9 Water bridges: C:Q.531, C:Y.533, C:K.590 Salt bridges: C:K.534, C:K.534 pi-Stacking: C:H.593

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

SO4.2: 4 residues within 4Å: Chain A: K.326, G.327 Chain B: N.12, M.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.327, A:A.328, B:M.13 Salt bridges: A:K.326 Water bridges: B:N.12 SO4.4: 4 residues within 4Å: Chain C: K.326, G.327 Chain D: N.12, M.13 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.327, C:A.328, D:M.13 Salt bridges: C:K.326 Water bridges: D:N.12

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: AC
Casein kinase II subunit alpha: 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

Casein kinase II subunit alpha

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