SMTL ID : 4ktr.2 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

1PE.1: 7 residues within 4Å: Chain A: K.65, G.68, K.69, R.371, E.389, C.391, P.392 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.65

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.366, E.375, G.376, E.447, R.450 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.375, A:E.375, A:G.376, A:G.376, A:R.450 Water bridges: A:R.366 GOL.3: 4 residues within 4Å: Chain A: T.555, I.556, I.557, K.561 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.555, A:I.557, A:K.561, A:K.561 GOL.4: 8 residues within 4Å: Chain A: A.319, R.320, Y.327, F.332, W.333, D.334, Q.475, L.624 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.320, A:D.334, A:Q.475 Water bridges: A:A.319, A:D.334, A:K.587, A:K.587 GOL.6: 4 residues within 4Å: Chain A: G.175, T.188, A.189, K.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.175 GOL.8: 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.9: 8 residues within 4Å: Chain A: P.310, K.313, S.314, L.315, Q.335, I.350, N.353, I.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.315, A:Q.335, A:N.353 Water bridges: A:N.353 GOL.12: 8 residues within 4Å: Chain B: Y.327, W.381, F.396, F.409, Q.475, K.587, I.667 Ligands: IFM.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.327, B:W.381, B:Q.475, B:K.587 GOL.14: 6 residues within 4Å: Chain B: R.366, E.375, G.376, E.447, R.450, I.516 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.375, B:G.376, B:E.447, B:R.450 GOL.15: 3 residues within 4Å: Chain B: D.152, E.230, A.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.152 Water bridges: B:D.152 GOL.16: 3 residues within 4Å: Chain B: P.182, E.212, R.223 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.223 Water bridges: B:E.212, B:E.212 GOL.17: 4 residues within 4Å: Chain B: D.539, H.541, I.543, Y.551 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.539, B:H.541 GOL.19: 6 residues within 4Å: Chain A: K.459 Chain B: Y.374, H.455, V.457, M.468, R.469 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.459, B:R.469, B:R.469 Water bridges: B:H.455, B:M.468 GOL.20: 7 residues within 4Å: Chain B: W.70, N.169, A.326, Y.327, Q.328, F.395, F.666 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.169, B:Y.327 Water bridges: B:E.72 GOL.21: 3 residues within 4Å: Chain B: D.363, R.366, R.367 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.367 GOL.22: 8 residues within 4Å: Chain B: P.310, V.311, K.313, S.314, L.315, I.350, N.353, I.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.315, B:Q.335 Water bridges: B:S.314, B:N.353

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.5: 18 residues within 4Å: Chain A: E.336, I.337, M.340, P.341, L.344, Y.345, Y.422, K.426, F.595, V.596, P.599, I.631, Q.635, Q.680, N.684, L.689, S.690, V.691 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.345, A:Y.422, A:P.599

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

PGE.7: 3 residues within 4Å: Chain A: E.721, D.723, R.756 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.10: 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.3, H2O.10 CA.23: 2 residues within 4Å: Chain B: E.213, D.214 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.214, H2O.22, H2O.24, H2O.25, H2O.25 CA.24: 1 residues within 4Å: Chain B: E.615 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.615, B:E.615, H2O.17, H2O.18, H2O.20

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

IFM.11: 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.12 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.332 Hydrogen bonds: B:R.320, B:W.333, B:W.333, B:Q.588 Water bridges: B:A.319, B:D.334, B:K.587, B:S.622

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

PG4.13: 9 residues within 4Å: Chain B: K.65, G.68, K.69, R.371, E.389, L.390, 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 7PE: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL(Non-functional Binders)

7PE.18: 14 residues within 4Å: Chain B: E.336, I.337, M.340, P.341, L.344, Y.422, V.596, P.599, I.631, V.632, Q.635, Q.680, N.684, L.689 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.422 Water bridges: B:Q.680

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
C

B
D

Glycoside hydrolase family 65 central catalytic

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