SMTL ID : 5npc.1

Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with unreacted alpha Cyclophellitol Cyclosulfate probe ME647

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: P.298, T.299, P.300, L.301, D.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.301, A:D.302 SO4.2: 4 residues within 4Å: Chain A: R.34, L.46, P.55, R.207 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.56 Salt bridges: A:R.34, A:R.207 SO4.3: 1 residues within 4Å: Chain A: R.773 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.773 SO4.4: 4 residues within 4Å: Chain A: T.708, D.709, N.710, Q.711 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.708, A:T.708, A:D.709, A:N.710, A:N.710 SO4.5: 4 residues within 4Å: Chain A: T.73, E.74, N.75, H.76 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.73, A:E.74, A:N.75, A:N.75, A:H.76 Salt bridges: A:H.76 SO4.6: 5 residues within 4Å: Chain A: E.728, R.729, G.783, R.784, E.785 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.784 Salt bridges: A:R.729, A:R.784 SO4.7: 5 residues within 4Å: Chain A: T.83, G.215, N.216, S.220, N.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.216, A:N.216, A:S.220, A:N.224 SO4.8: 1 residues within 4Å: Chain A: R.250 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.250, A:R.250 Salt bridges: A:R.250

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

EDO.9: 1 residues within 4Å: Chain A: T.781 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.781 EDO.10: 2 residues within 4Å: Chain A: D.659, R.661 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: R.566, F.570, F.586, D.589 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.566 EDO.12: 2 residues within 4Å: Chain A: T.763, P.764 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: K.347, F.349, E.350, P.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.347, A:E.350 EDO.14: 5 residues within 4Å: Chain A: Q.53, L.54, S.205, G.206, T.408 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.54, A:G.206 EDO.15: 4 residues within 4Å: Chain A: R.152, A.153, H.154, Q.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.163 EDO.16: 4 residues within 4Å: Chain A: W.292, D.293, K.294, K.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.292, A:K.294, A:K.327 EDO.17: 3 residues within 4Å: Chain A: K.281, H.286, E.295 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.286 EDO.18: 5 residues within 4Å: Chain A: F.362, S.363, K.364, S.367, R.416 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.362 Water bridges: A:S.367, A:R.416 EDO.19: 3 residues within 4Å: Chain A: S.39, E.40, Q.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40, A:Q.227 EDO.20: 1 residues within 4Å: Ligands: 94E.22 No protein-ligand interaction detected (PLIP)

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

PG4.21: 6 residues within 4Å: Chain A: L.539, L.542, R.545, W.617, Y.650, E.666 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.545, A:R.545 Water bridges: A:H.636

1 x 94E: (3~{a}~{R},4~{R},5~{S},6~{R},7~{R},7~{a}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydrobenzo[d][1,3,2]dioxathiole-4,5,6-triol(Non-covalent)

94E.22: 14 residues within 4Å: Chain A: Y.155, F.247, D.275, L.276, I.317, W.386, N.388, R.439, W.453, D.456, F.489, H.516, Q.518 Ligands: EDO.20 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.247, A:F.489 Hydrogen bonds: A:D.275, A:N.388, A:R.439, A:D.456, A:H.516 Water bridges: A:E.319, A:D.456, A:D.456

1 x OXL: OXALATE ION(Non-covalent)

OXL.23: 5 residues within 4Å: Chain A: A.673, H.707, S.740, R.774, K.793 8 PLIP interactions: 8 interactions with chain A Water bridges: A:H.707, A:D.741, A:Y.743, A:R.774 Salt bridges: A:H.707, A:R.774, A:K.793, A:K.793

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Artola, M. et al., 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor. ACS Cent Sci (2017)

Release Date

2017-08-09

Peptides

Oligosaccharide 4-alpha-D-glucosyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligosaccharide 4-alpha-D-glucosyltransferase

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