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

Crystal structure of 2-O-alpha-glucosylglycerol phosphorylase in complex with isofagomine and glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x IFM: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE(Non-covalent)

IFM.1: 10 residues within 4Å: Chain A: A.319, Y.327, F.332, W.333, D.334, Q.475, K.587, Q.588, L.624 Ligands: GOL.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.333, A:W.333, A:Q.475, A:K.587, A:Q.588 Water bridges: A:R.320, A:D.334 IFM.7: 11 residues within 4Å: Chain B: A.319, R.320, Y.327, F.332, W.333, D.334, W.381, Q.475, Q.588, L.624 Ligands: GOL.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.332 Hydrogen bonds: B:R.320, B:W.333, B:W.333, B:D.334, B:Q.588 Water bridges: B:S.622

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Y.327, W.381, F.395, F.396, F.409, Q.475, K.587 Ligands: IFM.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.327, A:Y.327, A:W.381, A:Q.475, A:K.587 GOL.3: 4 residues within 4Å: Chain A: K.605, E.608, E.612, K.638 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.605, A:K.605, A:K.638, A:K.638 GOL.4: 7 residues within 4Å: Chain A: Y.374, H.455, V.457, M.468, R.469 Chain B: K.459, M.468 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.468, A:R.469, B:K.459, B:K.459, B:R.462 Water bridges: A:H.455 GOL.8: 8 residues within 4Å: Chain B: Y.327, W.381, F.395, F.396, F.409, Q.475, K.587 Ligands: IFM.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.381, B:Q.475, B:K.587 GOL.10: 8 residues within 4Å: Chain B: W.70, N.169, A.326, Y.327, Q.328, F.395, T.665, F.666 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.169, B:N.169, B:Y.327, B:Q.328, B:F.666 GOL.11: 8 residues within 4Å: Chain B: P.310, K.313, S.314, L.315, I.317, I.350, N.353, I.354 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.310, B:S.314, B:L.315 GOL.12: 2 residues within 4Å: Chain B: E.213, D.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.214 Water bridges: B:D.214, B:D.214 GOL.13: 4 residues within 4Å: Chain B: Y.163, D.164, D.171, D.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.164, B:D.171, B:D.219, B:D.219

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 8 residues within 4Å: Chain A: K.65, G.68, K.69, R.371, E.389, C.391, P.392, D.393 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.65

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: E.615 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.615, A:E.615, H2O.4, H2O.8

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 8 residues within 4Å: Chain B: K.65, G.68, K.69, R.371, E.389, C.391, P.392, D.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.65 Water bridges: B:R.371

1 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.14: 20 residues within 4Å: Chain B: E.336, I.337, M.340, P.341, L.344, Y.345, Y.422, K.426, F.595, V.596, L.597, P.599, I.631, Q.635, I.636, Q.680, N.684, L.689, S.690, V.691 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.426 Hydrogen bonds: B:Y.345, B:Q.635, B:V.691

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Touhara, K.K. et al., Structural basis for reversible phosphorolysis and hydrolysis reactions of 2-O-alpha-glucosylglycerol phosphorylase. J.Biol.Chem. (2014)

Release Date

2014-05-21

Peptides

Glycoside hydrolase family 65 central catalytic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Glycoside hydrolase family 65 central catalytic

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