SMTL ID : 3v0q.1

Crystal structure of the Fucosylgalactoside alpha N-acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with UDP and H-antigen acceptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: UDP.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: 3 residues within 4Å: Chain B: D.155, D.157 Ligands: UDP.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:D.157, B:D.157, H2O.14

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

UDP.2: 16 residues within 4Å: Chain A: F.65, A.66, I.67, K.68, Y.70, V.128, R.132, D.155, V.156, D.157, K.290, H.292, R.296 Ligands: MN.1, BHE.3, GOL.4 15 PLIP interactions: 15 interactions with chain A 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, A:R.296, A:R.296 Salt bridges: A:K.290, A:K.290, A:R.296, A:R.296 pi-Stacking: A:Y.70 UDP.7: 16 residues within 4Å: Chain B: F.65, A.66, I.67, K.68, Y.70, V.128, R.132, D.155, V.156, D.157, K.290, H.292, R.296 Ligands: MN.6, BHE.8, GOL.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.128 Hydrogen bonds: B:F.65, B:F.65, B:I.67, B:I.67, B:V.156, B:D.157, B:D.157 Water bridges: B:R.132, B:R.296, B:R.296 Salt bridges: B:K.290, B:K.290, B:R.296, B:R.296 pi-Stacking: B:Y.70

2 x BHE: octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside(Non-covalent)

BHE.3: 13 residues within 4Å: Chain A: H.177, G.179, F.180, S.183, T.189, Y.208, W.244, E.247, D.270, L.273, H.292 Ligands: UDP.2, GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.180, A:D.270, A:L.273 Hydrogen bonds: A:T.189, A:E.247, A:D.270, A:K.290, A:H.292 Salt bridges: A:H.177, A:H.177 BHE.8: 13 residues within 4Å: Chain B: H.177, P.178, G.179, F.180, T.189, Y.208, W.244, E.247, D.270, L.273, H.292 Ligands: UDP.7, GOL.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.178, B:F.180, B:F.180, B:D.270, B:L.273 Hydrogen bonds: B:T.189, B:T.189, B:E.247, B:D.270, B:D.270, B:H.292 Salt bridges: B:H.177, B:H.177

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: W.125, S.129, W.244, H.245, D.246, E.247 Ligands: UDP.2, BHE.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.129, A:W.244, A:H.245, A:E.247 Water bridges: A:R.132 GOL.5: 5 residues within 4Å: Chain A: M.7, Q.52, F.53, Q.56 Chain B: T.260 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.56 Water bridges: A:V.8, A:V.8, A:Q.52, A:Q.52, A:Q.56 GOL.9: 8 residues within 4Å: Chain B: W.125, S.129, W.244, H.245, D.246, E.247 Ligands: UDP.7, BHE.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.129, B:W.244, B:E.247 Water bridges: B:R.132

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

SO4.10: 4 residues within 4Å: Chain B: R.120, A.121, Y.122, K.123 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.123 Water bridges: B:R.124, B:R.124 Salt bridges: B:R.120 SO4.11: 3 residues within 4Å: Chain B: R.54, N.57, R.90 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.57 Water bridges: B:R.54, B:R.54 Salt bridges: B:R.54, B:R.90

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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