SMTL ID : 2vs4.1

THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF alpha-1,3 GALACTOSYLTRANSFERASE (alpha3GT)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x NDG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG-GAL.1: 11 residues within 4Å: Chain A: Q.168, W.170, W.171, T.180, Y.199, H.201, W.235, E.238, W.277, K.280 Ligands: UDP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.168, A:T.180, A:H.201, A:K.280, A:Q.168, A:W.171 Water bridges: A:H.201, A:K.280, A:Y.282 Hydrophobic interactions: A:W.171 NDG-GAL.2: 10 residues within 4Å: Chain B: Q.168, W.170, W.171, T.180, Y.199, W.235, E.238, W.277, K.280 Ligands: UDP.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.168, B:T.180, B:E.238, B:K.280, B:Q.168, B:W.171 Water bridges: B:H.201, B:K.280, B:Y.282, B:Y.282 Hydrophobic interactions: B:W.171

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

MN.3: 4 residues within 4Å: Chain A: D.146, D.148, K.280 Ligands: UDP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.146, A:D.148, A:D.148, H2O.14 MN.6: 4 residues within 4Å: Chain B: D.146, D.148, K.280 Ligands: UDP.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.146, B:D.148, B:D.148, H2O.37

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

UDP.4: 16 residues within 4Å: Chain A: F.55, A.56, V.57, Y.60, W.116, I.119, S.120, R.123, D.146, V.147, D.148, K.280, Y.282, R.286 Ligands: NDG-GAL.1, MN.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.116, A:I.119 Hydrogen bonds: A:F.55, A:V.57, A:V.57, A:Y.60, A:R.123, A:V.147, A:D.148, A:D.148, A:Y.282 Water bridges: A:F.55, A:S.120, A:K.280, A:K.280, A:R.286, A:R.286 Salt bridges: A:K.280, A:K.280, A:R.286, A:R.286 pi-Stacking: A:Y.60 UDP.7: 16 residues within 4Å: Chain B: F.55, A.56, V.57, Y.60, W.116, I.119, S.120, R.123, D.146, V.147, D.148, K.280, Y.282, R.286 Ligands: NDG-GAL.2, MN.6 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:W.116, B:I.119 Hydrogen bonds: B:F.55, B:V.57, B:V.57, B:Y.60, B:Y.60, B:V.147, B:D.148, B:D.148 Water bridges: B:S.120, B:R.123, B:H.201, B:E.238, B:E.238, B:K.280, B:K.280, B:Y.282, B:R.286, B:R.286 Salt bridges: B:K.280, B:K.280, B:R.286, B:R.286 pi-Stacking: B:Y.60

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: K.47, Q.136, H.137, E.138, V.139, D.140 Chain B: K.47 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.47, A:K.47, A:H.137, A:D.140 Water bridges: A:T.49 GOL.8: 1 residues within 4Å: Chain B: K.221 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.218, B:K.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tumbale, P. et al., Structural Basis of Udp-Galactose Binding by Alpha- 1,3-Galactosyltransferase (Alpha3Gt): Role of Negative Charge on Aspartic Acid 316 in Structure and Activity. Biochemistry (2008)

Release Date

2008-07-15

Peptides

N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE