SMTL ID : 7p4c.1

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with noncovalent Cyclophellitol Sulfamidate probe KK131

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.543, R.546, F.617, W.618, Y.651 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.546, A:R.546 EDO.2: 6 residues within 4Å: Chain A: P.539, L.540, L.543, R.546, W.618 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.546 EDO.4: 3 residues within 4Å: Chain A: Y.156, Y.353 Ligands: 5OV.5 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: R.49, Q.54, L.55, S.206, G.207, R.208, T.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.55, A:G.207, A:G.207

1 x OXL: OXALATE ION(Non-covalent)

OXL.3: 5 residues within 4Å: Chain A: A.674, H.708, S.741, R.775, K.794 8 PLIP interactions: 8 interactions with chain A Water bridges: A:S.741, A:D.742, A:Y.744, A:R.775 Salt bridges: A:H.708, A:R.775, A:K.794, A:K.794

1 x 5OV: (3aR,4S,5S,6R,7R,7aS)-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3a,4,5,6,7,7a-hexahydro-3H-benzo[d][1,2,3]oxathiazole-4,5,6-triol(Non-covalent)

5OV.5: 15 residues within 4Å: Chain A: F.248, D.276, L.277, I.318, F.354, W.387, D.389, L.390, R.440, W.454, G.456, D.457, F.490, H.517 Ligands: EDO.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.276, A:D.389, A:D.389, A:R.440, A:W.454, A:D.457, A:D.457, A:H.517 Water bridges: A:D.457

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 6 residues within 4Å: Chain A: P.299, T.300, P.301, L.302, D.303, M.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.302, A:D.303 SO4.8: 4 residues within 4Å: Chain A: R.35, L.47, P.56, R.208 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.57 Salt bridges: A:R.35, A:R.208 SO4.9: 2 residues within 4Å: Chain A: D.530, E.531 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.531 Water bridges: A:D.530, A:E.532 SO4.10: 4 residues within 4Å: Chain A: T.709, D.710, N.711, Q.712 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.709, A:T.709, A:D.710, A:N.711, A:N.711, A:Q.712 SO4.11: 1 residues within 4Å: Chain A: R.251 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.251, A:R.251 Salt bridges: A:R.251 SO4.12: 2 residues within 4Å: Chain A: S.373, K.376 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.373 Salt bridges: A:K.376 SO4.13: 1 residues within 4Å: Chain A: K.337 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.337 SO4.14: 6 residues within 4Å: Chain A: A.42, T.84, G.216, N.217, S.221, N.225 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.84, A:N.217, A:N.217, A:S.221, A:N.225 SO4.15: 2 residues within 4Å: Chain A: E.729, R.730 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.730

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kok, K. et al., 1,6- epi-Cyclophellitol Cyclosulfamidate Is a Bona Fide Lysosomal alpha-Glucosidase Stabilizer for the Treatment of Pompe Disease. J.Am.Chem.Soc. (2022)

Release Date

2022-07-27

Peptides

Oligosaccharide 4-alpha-D-glucosyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Oligosaccharide 4-alpha-D-glucosyltransferase

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