SMTL ID : 4ee5.2 (4 other biounits)

Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with trisaccharide from Lacto-N-neotetraose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x BGC- GAL- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NAG.1: 12 residues within 4Å: Chain A: F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245, I.248 Ligands: GOL.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.244, A:F.245, A:I.248 Hydrogen bonds: A:Y.171, A:G.201, A:D.203, A:D.204, A:R.244 Water bridges: A:Y.174

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

UDP.2: 16 residues within 4Å: Chain A: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, D.235, N.238 Ligands: MN.3, GOL.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:P.72, A:R.74, A:R.74, A:R.76, A:V.138, A:D.139, A:D.235, A:D.235 Water bridges: A:R.74, A:K.164, A:K.164, A:K.164, A:K.164, A:N.238, A:N.238 Salt bridges: A:R.76, A:K.164, A:H.229, A:H.232, A:H.232 pi-Stacking: A:F.111 pi-Cation interactions: A:R.76

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

MN.3: 4 residues within 4Å: Chain A: D.139, H.229, H.232 Ligands: UDP.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.139, A:H.229, A:H.232

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.1, UDP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.200, A:E.202 Water bridges: A:G.198, A:G.200, A:N.238 GOL.5: 4 residues within 4Å: Chain A: F.73, R.74, N.75, N.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.75, A:N.75, A:N.104

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

SO4.6: 5 residues within 4Å: Chain A: E.33, F.34, N.35, R.228, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.34, A:R.231 Salt bridges: A:R.228 SO4.7: 3 residues within 4Å: Chain A: R.231, H.232, S.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.233 SO4.8: 2 residues within 4Å: Chain A: R.156, P.220 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.156 Salt bridges: A:R.156 SO4.9: 4 residues within 4Å: Chain A: N.49, Y.56, P.58, R.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.49, A:Y.56, A:R.59 Salt bridges: A:R.59 SO4.10: 5 residues within 4Å: Chain A: V.38, D.39, L.40, E.41, K.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.39, A:D.39, A:L.40, A:E.41 Salt bridges: A:K.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramakrishnan, B. et al., Binding of N-acetylglucosamine (GlcNAc) beta 1-6-branched oligosaccharide acceptors to beta 4-galactosyltransferase I reveals a new ligand binding mode. J.Biol.Chem. (2012)

Release Date

2012-07-04

Peptides

Beta-1,4-galactosyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-1,4-galactosyltransferase 1

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