SMTL ID : 4ktr.1 (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

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

IFM.1: 9 residues within 4Å: Chain A: A.319, R.320, Y.327, F.332, W.333, D.334, Q.475, Q.588, L.624 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.332 Hydrogen bonds: A:R.320, A:W.333, A:W.333, A:D.334, A:Q.588 Water bridges: A:D.334, A:Q.475, A:K.587, A: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, E.389, C.391, D.393, N.410 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.65

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.320, S.622, S.623, N.658, I.667, H.671 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.320, A:S.623, A:S.623 Water bridges: A:K.587, A:K.587 GOL.4: 9 residues within 4Å: Chain A: T.309, 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 Water bridges: A:S.314, A:Y.357 GOL.5: 3 residues within 4Å: Chain A: K.605, E.608, E.612 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.605, A:E.608, A:K.638, A:K.638 GOL.7: 2 residues within 4Å: Chain A: D.152, A.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.152, A:E.230, A:A.231 GOL.8: 4 residues within 4Å: Chain A: W.14, S.107, R.274, D.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.14, A:S.107, A:R.274, A:D.278 GOL.9: 5 residues within 4Å: Chain A: K.51, Y.163, D.164, H.176, D.219 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.51, A:K.51, A:D.219 Water bridges: A:Y.163, A:H.176 GOL.10: 9 residues within 4Å: Chain A: W.70, I.168, N.169, A.326, Y.327, Q.328, F.395, T.665, F.666 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.169, A:Y.327 Water bridges: A:Q.325 GOL.11: 4 residues within 4Å: Chain A: T.555, I.556, I.557, K.561 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.557, A:K.561 GOL.16: 7 residues within 4Å: Chain B: T.309, P.310, K.313, S.314, L.315, N.353, I.354 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.313, B:L.315 GOL.17: 8 residues within 4Å: Chain B: W.70, N.169, A.326, Y.327, Q.328, F.395, T.665, F.666 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.169, B:Y.327, B:Q.328, B:F.666 GOL.18: 3 residues within 4Å: Chain B: H.283, N.347, I.350 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.347, B:N.347 GOL.19: 5 residues within 4Å: Chain B: H.488, M.491, F.492, H.598, L.601 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.598 GOL.20: 7 residues within 4Å: Chain B: H.477, N.479, F.547, D.548, G.549, L.553, V.581 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.478, B:V.581 GOL.21: 7 residues within 4Å: Chain B: A.319, R.320, Y.327, F.332, W.333, D.334, L.624 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.320, B:W.333 Water bridges: B:D.334, B:D.334, B:Q.475

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

P6G.6: 14 residues within 4Å: Chain A: E.336, I.337, M.340, P.341, Y.422, F.595, V.596, P.599, V.607, I.631, Q.635, Q.680, N.684, L.689 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.599

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

PGE.12: 9 residues within 4Å: Chain A: L.81, L.83, D.158, G.160, I.161, Y.215, N.217, G.220, S.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.158, A:Y.215, A:N.217

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 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.2, H2O.7 CA.22: 1 residues within 4Å: Chain B: E.615 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.615, B:E.615, H2O.15, H2O.19

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

PG4.14: 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.15: 16 residues within 4Å: Chain B: E.336, I.337, M.340, P.341, L.344, Y.422, F.595, V.596, P.599, R.604, I.631, V.632, Q.635, Q.680, N.684, L.689 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.604

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
A

B
B

Glycoside hydrolase family 65 central catalytic

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