SMTL ID : 2ae7.4 (3 other biounits)

Crystal Structure of Human M340H-Beta1,4-Galactosyltransferase-I (M340H-B4GAL-T1) in Complex with Pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

2 x MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-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.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.245, A:I.248 Hydrogen bonds: A:Y.171, A:G.201, A:D.203, A:D.204, A:R.244 MAN-NAG.10: 12 residues within 4Å: Chain C: F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245, I.248 Ligands: GOL.31 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.245, C:I.248 Hydrogen bonds: C:G.201, C:D.203, C:D.204, C:D.204, C:R.244

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

MN.2: 4 residues within 4Å: Chain A: D.139, H.229, H.232 Ligands: UDH.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.139, A:H.229, A:H.232, H2O.1 MN.11: 4 residues within 4Å: Chain B: D.139, H.229, H.232 Ligands: UDH.18 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.139, B:H.229, B:H.232, H2O.8 MN.24: 4 residues within 4Å: Chain C: D.139, H.229, H.232 Ligands: UDH.29 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.139, C:H.229, C:H.232, H2O.15

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

SO4.3: 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 Salt bridges: A:R.228, A:R.231 SO4.4: 5 residues within 4Å: Chain A: N.49, Y.56, P.58, R.59 Chain C: R.231 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:R.231, A:Y.56, A:Y.56, A:R.59 Water bridges: C:R.228, A:R.59, A:D.60 Salt bridges: A:R.59 SO4.5: 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 SO4.6: 2 residues within 4Å: Chain A: H.232, S.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.233 SO4.12: 2 residues within 4Å: Chain B: R.156, P.220 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.156 Salt bridges: B:R.156 SO4.13: 6 residues within 4Å: Chain B: E.33, F.34, N.35, R.228, R.231 Chain C: R.59 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Salt bridges: C:R.59, B:R.228 Hydrogen bonds: B:F.34, B:R.231 SO4.14: 4 residues within 4Å: Chain B: N.49, Y.56, P.58, R.59 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.49, B:Y.56, B:Y.56, B:R.59, B:D.60 Water bridges: B:D.60, B:D.60 Salt bridges: B:R.59 SO4.15: 2 residues within 4Å: Chain B: H.232, S.233 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.233 Water bridges: B:H.79, B:R.231 SO4.16: 5 residues within 4Å: Chain B: V.38, D.39, L.40, E.41, K.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.39, B:L.40, B:E.41 Salt bridges: B:K.81 SO4.17: 2 residues within 4Å: Chain B: S.233, R.234 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.234 Salt bridges: B:R.234 SO4.25: 4 residues within 4Å: Chain C: N.49, Y.56, P.58, R.59 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.49, C:Y.56, C:R.59 Water bridges: C:D.60, C:D.60 Salt bridges: C:R.59 SO4.26: 5 residues within 4Å: Chain C: E.33, F.34, N.35, R.228, R.231 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.33, C:F.34 Salt bridges: C:R.228, C:R.231 SO4.27: 2 residues within 4Å: Chain C: H.232, S.233 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.233 SO4.28: 3 residues within 4Å: Chain C: S.233, R.234 Ligands: UDH.29 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.234 Salt bridges: C:R.234, C:K.236

3 x UDH: 6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE(Non-covalent)

UDH.7: 18 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, S.233, R.234, D.235, N.238 Ligands: MN.2, GOL.8 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:R.234 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:R.74, 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 UDH.18: 18 residues within 4Å: Chain B: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, R.234, D.235, N.238, P.240 Ligands: MN.11, GOL.19 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:W.199, B:R.234 Hydrogen bonds: B:P.72, B:R.74, B:R.74, B:R.76, B:V.138, B:D.139, B:D.235, B:D.235, B:N.238, B:N.238 Water bridges: B:R.74, B:D.137, B:D.137, B:K.164 Salt bridges: B:R.76, B:K.164, B:H.229, B:H.232, B:H.232 pi-Stacking: B:F.111 pi-Cation interactions: B:R.76 UDH.29: 19 residues within 4Å: Chain C: P.72, F.73, R.74, R.76, F.111, D.137, V.138, D.139, K.164, W.199, H.229, H.232, S.233, R.234, D.235, N.238 Ligands: MN.24, SO4.28, GOL.31 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:R.234 Hydrogen bonds: C:P.72, C:R.74, C:R.74, C:R.76, C:V.138, C:D.139, C:R.234, C:D.235, C:D.235 Water bridges: C:R.74, C:R.74, C:D.137, C:D.137, C:D.235 Salt bridges: C:R.76, C:K.164, C:H.232, C:H.232 pi-Stacking: C:F.111 pi-Cation interactions: C:R.76

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: R.113, W.199, G.200, E.202, D.203 Ligands: MAN-NAG.1, UDH.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.199, A:G.200, A:E.202 Water bridges: A:G.198, A:E.202 GOL.19: 7 residues within 4Å: Chain B: R.113, W.199, G.200, E.202, D.203 Ligands: MAN-MAN-NAG.9, UDH.18 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.199, B:G.200, B:E.202 Water bridges: B:G.177, B:G.177, B:G.198, B:E.202 GOL.20: 4 residues within 4Å: Chain B: Q.173, F.207, S.216, I.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.173, B:I.217 GOL.21: 4 residues within 4Å: Chain B: F.73, R.74, N.75, N.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.75, B:N.75, B:N.104 GOL.22: 5 residues within 4Å: Chain B: N.195, W.197, R.247, P.286, S.287 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.197, B:R.247, B:R.247, B:S.287, B:S.287 Water bridges: B:Q.243 GOL.23: 6 residues within 4Å: Chain B: M.36, P.37, V.38, D.39, L.42, Y.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.39, B:D.39, B:Y.85 GOL.31: 7 residues within 4Å: Chain C: R.113, W.199, G.200, E.202, D.203 Ligands: MAN-NAG.10, UDH.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.199, C:G.200 Water bridges: C:G.198, C:G.200

1 x MAN- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose

MAN-MAN-NAG.9: 13 residues within 4Å: Chain B: F.165, P.170, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245, I.248 Ligands: GOL.19 9 PLIP interactions: 9 interactions with chain B Water bridges: B:R.244, B:Y.174 Hydrophobic interactions: B:F.245, B:I.248 Hydrogen bonds: B:Y.171, B:G.201, B:D.203, B:D.204, B:D.204, B:R.244

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.30: 5 residues within 4Å: Chain C: N.195, W.197, R.247, P.286, S.287 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.247, C:S.287, C:S.287

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramasamy, V. et al., Oligosaccharide Preferences of beta1,4-Galactosyltransferase-I: Crystal Structures of Met340His Mutant of Human beta1,4-Galactosyltransferase-I with a Pentasaccharide and Trisaccharides of the N-Glycan Moiety. J.Mol.Biol. (2005)

Release Date

2005-10-04

Peptides

Beta-1,4-galactosyltransferase 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Beta-1,4-galactosyltransferase 1

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