SMTL ID : 8rw3.1 (2 other biounits)

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with a non-covalent 1,2- Cyclophellitol aziridine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

GDQ.1: 10 residues within 4Å: Chain A: F.271, D.299, I.341, W.410, D.412, R.463, W.477, D.480, F.513, H.540 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.271, A:F.513 Hydrogen bonds: A:D.299, A:D.299, A:R.463, A:D.480, A:H.540

1 x OXL: OXALATE ION(Non-covalent)

OXL.2: 4 residues within 4Å: Chain A: H.731, S.764, R.798, K.817 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.798 Water bridges: A:N.762, A:S.764, A:S.764, A:Y.767, A:R.798 Salt bridges: A:H.731, A:K.817, A:K.817

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

SO4.3: 4 residues within 4Å: Chain A: T.323, P.324, L.325, D.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.325, A:D.326 SO4.4: 4 residues within 4Å: Chain A: T.732, D.733, N.734, Q.735 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.732, A:T.732, A:D.733, A:N.734 SO4.5: 2 residues within 4Å: Chain A: R.58, R.231 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.80 Salt bridges: A:R.58, A:R.231 SO4.8: 2 residues within 4Å: Chain A: D.553, E.554 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.554

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

EDO.6: 4 residues within 4Å: Chain A: H.178, H.184, S.185, G.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.184, A:G.186

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

PG4.7: 5 residues within 4Å: Chain A: R.569, F.640, W.641, Y.674, E.690 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.690

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ofman, T.P. et al., Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining alpha-Glucosidase Inhibition. Chemistry (2024)

Release Date

2024-05-15

Peptides

Oligosaccharide 4-alpha-D-glucosyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Oligosaccharide 4-alpha-D-glucosyltransferase

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