SMTL ID : 1r7y.2 (1 other biounit)

Glycosyltransferase A in complex with 3-amino-acceptor analog inhibitor and uridine diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x AIG- FUC: alpha-L-fucopyranose-(1-2)-hexyl 3-amino-3-deoxy-beta-D-galactopyranoside(Non-covalent)

AIG-FUC.1: 11 residues within 4Å: Chain A: H.171, P.172, F.174, T.183, Y.202, W.238, E.241, D.264, L.267, L.268 Ligands: UDP.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.172, A:D.264, A:L.267, A:L.268 Hydrogen bonds: A:T.183, A:E.241, A:D.264, A:D.264 Salt bridges: A:H.171 AIG-FUC.9: 11 residues within 4Å: Chain B: H.171, P.172, F.174, T.183, Y.202, W.238, E.241, D.264, L.267, L.268 Ligands: UDP.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.172, B:D.264, B:L.267, B:L.268 Hydrogen bonds: B:T.183, B:T.183, B:E.241, B:D.264 Salt bridges: B:H.171

10 x HG: MERCURY (II) ION(Non-covalent)

HG.2: 4 residues within 4Å: Chain A: C.222, H.223, M.226, D.240 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.222, A:D.240 HG.3: 3 residues within 4Å: Chain A: L.218, C.222, D.240 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.222, H2O.6 HG.4: 2 residues within 4Å: Chain A: T.57, C.147 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.57, A:C.147, H2O.6 HG.5: 2 residues within 4Å: Chain A: C.18, G.36 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.18, A:G.36 HG.6: 2 residues within 4Å: Chain A: C.147, V.148 No protein-ligand interaction detected (PLIP) HG.10: 4 residues within 4Å: Chain B: C.222, H.223, M.226, D.240 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.222, B:D.240 HG.11: 3 residues within 4Å: Chain B: L.218, C.222, D.240 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.222, H2O.11 HG.12: 2 residues within 4Å: Chain B: T.57, C.147 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.57, B:C.147, H2O.11 HG.13: 2 residues within 4Å: Chain B: C.18, G.36 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.18, B:G.36 HG.14: 2 residues within 4Å: Chain B: C.147, V.148 No protein-ligand interaction detected (PLIP)

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

MN.7: 4 residues within 4Å: Chain A: D.149, D.151, M.152 Ligands: UDP.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.151, A:D.151 MN.15: 4 residues within 4Å: Chain B: D.149, D.151, M.152 Ligands: UDP.16 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.151, B:D.151

2 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.8: 12 residues within 4Å: Chain A: F.59, A.60, I.61, K.62, K.63, Y.64, D.149, V.150, D.151 Ligands: AIG-FUC.1, AIG-FUC.1, MN.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:F.59, A:I.61, A:I.61, A:Y.64, A:Y.64, A:V.150, A:D.151 Water bridges: A:F.59 pi-Stacking: A:Y.64 UDP.16: 12 residues within 4Å: Chain B: F.59, A.60, I.61, K.62, K.63, Y.64, D.149, V.150, D.151 Ligands: AIG-FUC.9, AIG-FUC.9, MN.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:F.59, B:I.61, B:I.61, B:Y.64, B:D.149, B:V.150, B:D.151 Water bridges: B:F.59 pi-Stacking: B:Y.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, H.P. et al., The influence of an intramolecular hydrogen bond in differential recognition of inhibitory acceptor analogs by human ABO(H) blood group A and B glycosyltransferases. J.Biol.Chem. (2003)

Release Date

2004-02-10

Peptides

Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase

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