SMTL ID : 5c4d.1

Crystal structure of GTB + UDP-Glc + DI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.154, D.156 Ligands: UPG.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.154, A:D.156, A:D.156, H2O.3, H2O.9 MN.5: 3 residues within 4Å: Chain B: D.154, D.156 Ligands: UPG.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.154, B:D.156, B:D.156, H2O.14, H2O.19

2 x DA8: octyl 3-deoxy-2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-xylo-hexopyranoside(Non-covalent)

DA8.2: 13 residues within 4Å: Chain A: H.176, S.178, F.179, T.188, Y.207, M.209, W.243, E.246, D.269, L.272, A.286, K.289 Ligands: UPG.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.243, A:D.269, A:L.272, A:L.272 Hydrogen bonds: A:S.178, A:T.188, A:T.188, A:E.246, A:D.269, A:K.289 Water bridges: A:D.269 Salt bridges: A:H.176, A:H.176 DA8.6: 13 residues within 4Å: Chain B: H.176, S.178, F.179, T.188, Y.207, M.209, W.243, E.246, D.269, L.272, A.286, K.289 Ligands: UPG.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.243, B:D.269, B:L.272, B:L.272 Hydrogen bonds: B:S.178, B:T.188, B:E.246, B:D.269, B:D.269, B:K.289 Water bridges: B:D.269 Salt bridges: B:H.176, B:H.176

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

UPG.3: 16 residues within 4Å: Chain A: F.64, A.65, I.66, Y.69, R.131, D.154, V.155, D.156, M.209, G.210, A.211, D.245, E.246, K.289 Ligands: MN.1, DA8.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:F.64, A:I.66, A:I.66, A:Y.69, A:R.131, A:V.155, A:D.156, A:G.210, A:G.210, A:A.211 Water bridges: A:R.131, A:D.154, A:H.244 Salt bridges: A:K.289, A:K.289 pi-Stacking: A:Y.69 UPG.7: 16 residues within 4Å: Chain B: F.64, A.65, I.66, Y.69, R.131, D.154, V.155, D.156, M.209, G.210, A.211, D.245, E.246, K.289 Ligands: MN.5, DA8.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:F.64, B:I.66, B:I.66, B:Y.69, B:Y.69, B:R.131, B:D.154, B:V.155, B:D.156, B:G.210, B:G.210, B:A.211 Water bridges: B:R.131, B:D.154 Salt bridges: B:K.289, B:K.289 pi-Stacking: B:Y.69

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 5 residues within 4Å: Chain A: I.45, K.82, H.83, V.86, H.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.82, A:H.162 PG0.8: 5 residues within 4Å: Chain B: I.45, K.82, H.83, V.86, H.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.82 Water bridges: B:H.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gagnon, S.M. et al., High Resolution Structures of the Human ABO(H) Blood Group Enzymes in Complex with Donor Analogs Reveal That the Enzymes Utilize Multiple Donor Conformations to Bind Substrates in a Stepwise Manner. J.Biol.Chem. (2015)

Release Date

2015-09-23

Peptides

Histo-blood group ABO system transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Histo-blood group ABO system transferase

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