SMTL ID : 5npd.1

Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Aziridine probe CF021

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

7 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: 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:Q.711 SO4.4: 2 residues within 4Å: Chain A: D.529, E.530 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.530 SO4.5: 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 SO4.6: 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 SO4.7: 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

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

PG4.8: 5 residues within 4Å: Chain A: P.538, L.542, R.545, Y.650, E.666 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.545, A:R.545

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

EDO.9: 2 residues within 4Å: Chain A: D.659, R.661 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.659, A:R.661 EDO.10: 1 residues within 4Å: Chain A: D.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.427 EDO.11: 2 residues within 4Å: Chain A: E.785, A.786 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.786 Water bridges: A:R.718 EDO.12: 6 residues within 4Å: Chain A: Q.53, L.54, S.205, G.206, R.207, T.408 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.54, A:G.206 EDO.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain A: R.566, F.570, F.586, G.588, D.589 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.566, A:G.588 Water bridges: A:K.643

1 x 94B: (1~{S},2~{S},3~{S},4~{R},5~{R},6~{S})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol(Non-covalent)

94B.15: 11 residues within 4Å: Chain A: F.247, D.275, L.276, I.317, W.386, N.388, R.439, W.453, D.456, F.489, H.516 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.247, A:F.489 Hydrogen bonds: A:D.275, A:N.388, A:R.439, A:W.453, A:D.456, A:H.516 Water bridges: A:D.456

1 x OXL: OXALATE ION(Non-covalent)

OXL.16: 5 residues within 4Å: Chain A: A.673, H.707, S.740, R.774, K.793 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.774 Water bridges: A:H.707, A:S.740, A:D.741, A:Y.743 Salt bridges: A:H.707, 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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