SMTL ID : 4ktr.3 (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: 9 residues within 4Å: Chain A: A.319, Y.327, F.332, W.333, D.334, W.381, Q.475, Q.588, L.624 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.332 Hydrogen bonds: A:Y.327, A:W.333, A:W.333, A:D.334, A:Q.588 Water bridges: A:R.320, A:Q.475 IFM.9: 10 residues within 4Å: Chain B: A.319, Y.327, F.332, W.333, D.334, W.381, Q.475, Q.588, L.624 Ligands: GOL.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.332 Hydrogen bonds: B:R.320, B:W.333, B:W.333, B:K.587, B:K.587, B:Q.588 Water bridges: B:D.334, B:D.334, B:S.622

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 8 residues within 4Å: Chain A: K.65, G.68, K.69, R.371, C.391, P.392, D.393, N.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.65

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.3: 13 residues within 4Å: Chain A: E.336, I.337, M.340, P.341, Y.422, F.595, V.596, P.599, I.631, Q.635, Q.680, N.684, L.689 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.366, E.375, G.376, E.447, R.450, I.516 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.375, A:G.376, A:R.450 Water bridges: A:G.376 GOL.5: 8 residues within 4Å: Chain A: D.398, L.400, Y.572, G.574, P.576, N.577, G.578 Chain B: R.403 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.572, A:Y.572, A:N.577, B:R.403 Water bridges: B:S.401 GOL.6: 8 residues within 4Å: Chain A: W.70, N.169, A.326, Y.327, Q.328, F.395, T.665, F.666 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.169, A:Y.327, A:Q.328 Water bridges: A:Q.325 GOL.7: 9 residues within 4Å: Chain A: P.310, K.313, S.314, L.315, I.317, Q.335, I.350, N.353, I.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.313, A:Q.335 GOL.10: 8 residues within 4Å: Chain B: Y.327, W.381, F.395, F.396, F.409, Q.475, K.587 Ligands: IFM.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.327, B:Y.327, B:W.381, B:Q.475, B:K.587, B:K.587 GOL.12: 8 residues within 4Å: Chain B: P.310, K.313, S.314, L.315, I.317, Q.335, N.353, I.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.313, B:Q.335 Water bridges: B:P.310, B:N.353 GOL.13: 2 residues within 4Å: Chain B: E.213, D.214 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.214

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 1 residues within 4Å: Chain A: E.615 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.615, A:E.615, H2O.4, H2O.7, H2O.7

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

PG4.11: 8 residues within 4Å: Chain B: K.65, G.68, K.69, R.371, E.389, C.391, P.392, D.393 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.65

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

PGE.14: 9 residues within 4Å: Chain B: E.336, I.337, M.340, P.341, L.344, Y.422, V.596, Q.680, N.684 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.596

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
E

B
F

Glycoside hydrolase family 65 central catalytic

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