SMTL ID : 3v0n.1

Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with a novel UDP-GalNAc derived inhibitor (3GW and 4GW)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.155, D.157 Ligands: 4GW.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:D.157, A:D.157, H2O.5 MN.6: 4 residues within 4Å: Chain B: D.155, D.157 Ligands: 3GW.7, 4GW.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, B:D.157, H2O.15, H2O.21

2 x 4GW: 5-(5-formylthiophen-2-yl)uridine 5'-(trihydrogen diphosphate)(Non-covalent)

4GW.2: 11 residues within 4Å: Chain A: F.65, A.66, I.67, Y.70, W.125, V.128, R.132, D.155, V.156, D.157 Ligands: MN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.125 Hydrogen bonds: A:F.65, A:F.65, A:I.67, A:I.67, A:Y.70, A:V.156, A:D.157 Water bridges: A:R.132 pi-Stacking: A:Y.70 4GW.8: 12 residues within 4Å: Chain B: F.65, A.66, I.67, Y.70, W.125, V.128, R.132, D.155, V.156, D.157 Ligands: MN.6, 3GW.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.125 Hydrogen bonds: B:F.65, B:F.65, B:I.67, B:I.67, B:Y.70, B:Y.70, B:V.156, B:D.157 Water bridges: B:R.132, B:D.155, B:D.155 pi-Stacking: B:Y.70

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.177, F.180, T.189, Y.208, W.244, E.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.189, A:T.189, A:E.247 GOL.9: 7 residues within 4Å: Chain B: H.177, F.180, T.189, Y.208, W.244, E.247 Ligands: 3GW.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.189, B:E.247

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

SO4.4: 2 residues within 4Å: Chain A: T.110, G.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.110, A:G.111 Water bridges: A:G.109 SO4.5: 3 residues within 4Å: Chain A: R.120, Y.122, K.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.123 Water bridges: A:R.124 Salt bridges: A:R.120 SO4.10: 2 residues within 4Å: Chain B: S.115, R.143 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.115 Water bridges: B:S.115, B:V.116, B:R.143 Salt bridges: B:R.143

1 x 3GW: 5-(5-formylthiophen-2-yl)uridine-5'(2-(acetylamino)-2-deoxy-alpha-D-galactosyl)-diphosphate(Non-covalent)

3GW.7: 21 residues within 4Å: Chain B: F.65, A.66, I.67, Y.70, W.125, V.128, R.132, D.155, V.156, D.157, H.177, P.178, G.211, A.212, W.244, E.247, L.268, W.269 Ligands: MN.6, 4GW.8, GOL.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.125 Hydrogen bonds: B:F.65, B:I.67, B:I.67, B:Y.70, B:D.155, B:V.156, B:D.157, B:G.211, B:A.212, B:E.247 Water bridges: B:S.129, B:S.129, B:R.132, B:D.155, B:E.247 pi-Stacking: B:Y.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jrgensen, R. et al., Base-modified donor analogues reveal novel dynamic features of a glycosyltransferase. J.Biol.Chem. (2013)

Release Date

2013-01-23

Peptides

Histo-blood group ABO system transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histo-blood group ABO system transferase

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