SMTL ID : 2wtx.1 (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

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: E.272, P.403, Y.404, D.405, R.406 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.403, A:R.406, A:R.406 Water bridges: A:D.405 EDO.2: 4 residues within 4Å: Chain A: N.78, R.301, G.302, D.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.78, A:N.78, A:G.302, A:D.303

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

UDP.3: 16 residues within 4Å: Chain A: A.21, G.22, G.23, V.26, V.261, R.263, K.268, H.339, F.340, R.342, L.345, N.365, L.366, V.367, E.370 Ligands: VDO.4 15 PLIP interactions: 15 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:R.263, A:N.365 Salt bridges: A:R.263, A:K.268, A:K.268 UDP.5: 13 residues within 4Å: Chain B: V.261, R.263, K.268, P.298, H.339, F.340, R.342, L.345, N.365, L.366, V.367, E.370 Ligands: VDO.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.261 Hydrogen bonds: B:F.340, B:F.340, B:N.365, B:L.366, B:V.367, B:E.370 Water bridges: B:R.263, 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.4: 21 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, I.226, R.263, R.301, D.362, G.363, M.364, N.365, L.366 Ligands: UDP.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.155 Hydrogen bonds: A:G.23, A:Y.77, A:D.131, A:D.131, A:H.155, A:D.362, A:G.363, A:M.364, A:N.365, A:L.366 Water bridges: A:R.10, A:N.82, A:R.301 Salt bridges: A:R.10, A:R.301 VDO.6: 16 residues within 4Å: Chain B: W.86, D.131, H.133, H.155, I.156, Q.186, I.226, R.263, S.300, R.301, D.362, G.363, M.364, N.365, L.366 Ligands: UDP.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.155 Hydrogen bonds: B:Y.77, B:Y.77, B:D.131, B:D.131, B:H.155, B:Q.186, B:D.362, B:G.363, B:M.364, B:N.365, B:L.366 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
B

B
C

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

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