SMTL ID : 3sx3.2 (1 other biounit)

Crystal structure of AABB+UDP+Gal with glycerol as the cryoprotectant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 17 residues within 4Å: Chain A: F.60, A.61, I.62, K.63, Y.65, V.123, S.124, R.127, D.150, V.151, D.152, K.285, H.287, R.291 Ligands: GOL.2, GAL.3, MN.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.123 Hydrogen bonds: A:F.60, A:F.60, A:I.62, A:I.62, A:Y.65, A:V.151, A:D.152 Water bridges: A:R.127, A:R.291, A:R.291 Salt bridges: A:K.285, A:K.285, A:H.287, A:R.291, A:R.291 pi-Stacking: A:Y.65 UDP.6: 17 residues within 4Å: Chain B: F.60, A.61, I.62, K.63, Y.65, V.123, S.124, R.127, D.150, V.151, D.152, K.285, H.287, R.291 Ligands: GOL.7, GAL.8, MN.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.123 Hydrogen bonds: B:F.60, B:F.60, B:I.62, B:I.62, B:Y.65, B:Y.65, B:V.151, B:D.152 Water bridges: B:R.127, B:R.291, B:R.291 Salt bridges: B:K.285, B:K.285, B:H.287, B:R.291, B:R.291 pi-Stacking: B:Y.65

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: W.120, S.124, R.127, W.239, H.240, D.241, E.242 Ligands: UDP.1, GAL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.124, A:H.240, A:D.241, A:E.242 Water bridges: A:R.127, A:R.127 GOL.7: 9 residues within 4Å: Chain B: W.120, S.124, R.127, W.239, H.240, D.241, E.242 Ligands: UDP.6, GAL.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.124, B:D.241, B:E.242 Water bridges: B:R.127, B:R.127

2 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.3: 8 residues within 4Å: Chain A: H.172, F.175, T.184, Y.203, W.239, E.242 Ligands: UDP.1, GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.184, A:T.184, A:E.242 Salt bridges: A:H.172 GAL.8: 8 residues within 4Å: Chain B: H.172, F.175, T.184, Y.203, W.239, E.242 Ligands: UDP.6, GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.184, B:E.242 Salt bridges: B:H.172

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: Q.51, N.52, D.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.52 PEG.9: 3 residues within 4Å: Chain B: Q.51, N.52, D.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.52 Water bridges: B:D.144

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

MN.5: 3 residues within 4Å: Chain A: D.150, D.152 Ligands: UDP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.150, A:D.152, A:D.152, H2O.2 MN.10: 3 residues within 4Å: Chain B: D.150, D.152 Ligands: UDP.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.150, B:D.152, B:D.152, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johal, A.R. et al., Sequence-dependent effects of cryoprotectants on the active sites of the human ABO(H) blood group A and B glycosyltransferases. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-02-29

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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