SMTL ID : 7p4d.1

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with covalent Cyclophellitol Sulfamidate probe KK130

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: K.53, Q.54, L.55, S.206, G.207, R.208, T.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.55, A:G.207 EDO.4: 4 residues within 4Å: Chain A: Y.156, Y.353, E.394 Ligands: 56I.5 No protein-ligand interaction detected (PLIP)

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

PG4.2: 9 residues within 4Å: Chain A: P.539, L.540, L.543, R.546, F.617, W.618, Y.651, E.667, H.669 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.546, A:R.546

1 x OXL: OXALATE ION(Non-covalent)

OXL.3: 6 residues within 4Å: Chain A: A.674, H.708, S.741, Q.743, R.775, K.794 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.743 Water bridges: 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 56I: [(1R,2R,3R,4R,5S)-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)cyclohexyl]sulfamic acid(Covalent)

56I.5: 17 residues within 4Å: Chain A: Y.156, F.248, D.276, L.277, I.318, E.320, F.354, W.387, D.389, L.390, R.440, W.454, G.456, D.457, F.490, H.517 Ligands: EDO.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.389, A:L.390 Hydrogen bonds: A:D.276, A:R.440, A:W.454, A:D.457, A:D.457, A:H.517 Water bridges: A:R.440, A:D.457, A:D.457

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

SO4.6: 5 residues within 4Å: Chain A: P.299, T.300, P.301, L.302, D.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.302, A:D.303 SO4.7: 5 residues within 4Å: Chain A: R.35, L.47, P.56, S.57, R.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.57 Salt bridges: A:R.35, A:R.208 SO4.8: 2 residues within 4Å: Chain A: D.530, E.531 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.531 Water bridges: A:D.530 SO4.9: 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 SO4.10: 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 SO4.11: 2 residues within 4Å: Chain A: R.622, Q.624 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.624 Salt bridges: A:R.622 SO4.12: 5 residues within 4Å: Chain A: T.74, E.75, N.76, H.77, R.88 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:E.75, A:N.76, A:N.76, A:H.77, A:R.88 Salt bridges: A:H.77 SO4.13: 1 residues within 4Å: Chain A: K.337 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.337 Salt bridges: A:K.337

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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