SMTL ID : 2wtx.2 (1 other biounit)

Insight into the mechanism of enzymatic glycosyltransfer with retention through the synthesis and analysis of bisubstrate glycomimetics of trehalose-6-phosphate synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: T.299, S.300, R.301, G.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.301, A:G.302 EDO.2: 5 residues within 4Å: Chain A: H.90, R.92, L.360, R.361, Y.404 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.92 EDO.3: 5 residues within 4Å: Chain A: D.181, A.218, F.219, R.220, I.454 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.181, A:D.181

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

UDP.4: 18 residues within 4Å: Chain A: A.21, G.22, G.23, V.26, V.261, R.263, K.268, I.296, P.298, H.339, F.340, R.342, L.345, N.365, L.366, V.367, E.370 Ligands: VDO.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.21, A:V.261 Hydrogen bonds: A:G.22, A:G.23, A:F.340, A:F.340, A:N.365, A:L.366, A:V.367, A:E.370 Water bridges: A:S.267, A:K.268, A:N.365 Salt bridges: A:R.263, A:K.268, A:K.268 UDP.6: 14 residues within 4Å: Chain B: V.261, R.263, K.268, P.298, H.339, F.340, R.342, L.345, M.346, N.365, L.366, V.367, E.370 Ligands: VDO.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.261, B:P.298 Hydrogen bonds: B:F.340, B:F.340, B:L.366, B:V.367, B:E.370 Water bridges: B:R.263, B:R.263, B:S.267, B:N.365 Salt bridges: B:R.263, B:K.268, B:K.268

2 x VDO: [(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

VDO.5: 22 residues within 4Å: Chain A: R.10, A.21, G.22, G.23, L.24, Y.77, W.86, D.131, Y.132, H.133, H.155, I.156, Q.186, I.226, R.263, R.301, D.362, G.363, M.364, N.365, L.366 Ligands: UDP.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:H.155 Hydrogen bonds: A:G.23, A:Y.77, A:Y.77, A:Y.77, A:D.131, A:Y.132, A:D.362, A:G.363, A:M.364, A:N.365, A:L.366 Water bridges: A:R.10, A:R.10, A:L.24, A:N.82, A:H.133, A:K.268, A:R.301, A:D.362, A:D.362 Salt bridges: A:R.10, A:R.301 VDO.7: 18 residues within 4Å: Chain B: L.24, Y.77, W.86, D.131, Y.132, H.133, H.155, I.156, Q.186, I.226, R.263, R.301, D.362, G.363, M.364, N.365, L.366 Ligands: UDP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:H.155 Hydrogen bonds: B:Y.77, B:D.131, B:D.362, B:D.362, B:G.363, B:M.364, B:N.365, B:L.366 Water bridges: B:K.268, B:R.301 Salt bridges: B:R.263, B:R.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Errey, J.C. et al., Mechanistic Insight Into Enzymatic Glycosyl Transfer with Retention of Configuration Through Analysis of Glycomimetic Inhibitors. Angew.Chem.Int.Ed.Engl. (2010)

Release Date

2010-02-23

Peptides

ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]

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