SMTL ID : 5c4e.1

Crystal structure of GTB + UDP-Glc + H-antigen acceptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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: UDP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.154, A:D.156, A:D.156, H2O.8 MN.5: 3 residues within 4Å: Chain B: D.154, D.156 Ligands: UDP.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.154, B:D.156, B:D.156, H2O.19

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

UDP.2: 14 residues within 4Å: Chain A: F.64, A.65, I.66, K.67, Y.69, R.131, D.154, V.155, D.156, K.289, H.291, R.295 Ligands: MN.1, 4YA.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:F.64, A:I.66, A:I.66, A:V.155, A:D.156 Water bridges: A:F.64 Salt bridges: A:K.289, A:K.289, A:R.295, A:R.295 pi-Stacking: A:Y.69 UDP.6: 14 residues within 4Å: Chain B: F.64, A.65, I.66, K.67, Y.69, R.131, D.154, V.155, D.156, K.289, H.291, R.295 Ligands: MN.5, 4YA.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:F.64, B:I.66, B:I.66, B:Y.69, B:V.155, B:D.156 Water bridges: B:F.64 Salt bridges: B:K.289, B:K.289, B:R.295, B:R.295 pi-Stacking: B:Y.69

2 x 4YA: hexyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside(Non-covalent)

4YA.3: 14 residues within 4Å: Chain A: H.176, P.177, S.178, F.179, T.188, Y.207, M.209, W.243, E.246, D.269, L.272, A.286, H.291 Ligands: UDP.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.177, A:L.272 Hydrogen bonds: A:S.178, A:T.188, A:T.188, A:E.246, A:D.269, A:K.289, A:H.291 Water bridges: A:E.246, A:E.246 Salt bridges: A:H.176, A:H.176 4YA.7: 14 residues within 4Å: Chain B: H.176, P.177, S.178, F.179, T.188, Y.207, M.209, W.243, E.246, D.269, L.272, A.286, H.291 Ligands: UDP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.177, B:L.272 Hydrogen bonds: B:S.178, B:T.188, B:E.246, B:D.269, B:D.269, B:K.289, B:H.291 Water bridges: B:E.246, B:E.246 Salt bridges: B:H.176, B:H.176

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.82, A:H.162 Water bridges: A:V.86 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:V.86

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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