SMTL ID : 4kc1.1

Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 2 residues within 4Å: Chain A: D.157 Ligands: WS1.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.157, H2O.1, H2O.5, H2O.10 MN.4: 2 residues within 4Å: Chain B: D.157 Ligands: WS1.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.157, H2O.16, H2O.21, H2O.25

2 x BHE: octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside(Non-covalent)

BHE.2: 12 residues within 4Å: Chain A: H.177, G.179, F.180, S.183, T.189, Y.208, W.244, E.247, D.270, L.273, A.287 Ligands: WS1.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.180, A:D.270 Hydrogen bonds: A:T.189, A:E.247, A:D.270 Salt bridges: A:H.177, A:H.177 BHE.5: 12 residues within 4Å: Chain B: H.177, G.179, F.180, S.183, T.189, Y.208, W.244, E.247, D.270, L.273, A.287 Ligands: WS1.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.180, B:D.270 Hydrogen bonds: B:T.189, B:T.189, B:E.247 Salt bridges: B:H.177, B:H.177

2 x WS1: 6-(1-beta-D-Glucopyranosyloxymethyl)-N-(5'-deoxyluridine-5'-yl)picolinamide(Non-covalent)

WS1.3: 12 residues within 4Å: Chain A: F.65, A.66, I.67, K.68, Y.70, V.128, R.132, D.155, V.156, D.157 Ligands: MN.1, BHE.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.128 Hydrogen bonds: A:F.65, A:F.65, A:I.67, A:I.67, A:Y.70, A:V.156, A:D.157, A:D.157 Water bridges: A:K.68, A:S.129, A:S.129, A:S.129, A:R.132, A:D.155 pi-Stacking: A:Y.70 WS1.6: 12 residues within 4Å: Chain B: F.65, A.66, I.67, K.68, Y.70, V.128, R.132, D.155, V.156, D.157 Ligands: MN.4, BHE.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.128 Hydrogen bonds: B:F.65, B:F.65, B:I.67, B:I.67, B:V.156, B:D.157, B:D.157 Water bridges: B:K.68, B:S.129, B:S.129, B:S.129, B:R.132 pi-Stacking: B:Y.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate. Chemistry (2013)

Release Date

2013-09-11

Peptides

Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase

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