SMTL ID : 4ee3.5 (4 other biounits)

Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with pentasaccharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x BGC- GAL- NAG- GAL- NAG: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NAG-GAL-NAG.1: 11 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 Ligands: GOL.14 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.164, A:K.164, A:K.164 Hydrogen bonds: A:Y.171, A:G.201, A:D.203, A:D.204, A:R.244 BGC-GAL-NAG-GAL-NAG.2: 11 residues within 4Å: Chain B: F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: GOL.23 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.244, B:F.245 Hydrogen bonds: B:Y.171, B:G.201, B:D.203, B:D.204, B:D.204, B:R.244 Water bridges: B:Y.174, B:Y.174 BGC-GAL-NAG-GAL-NAG.3: 11 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 Ligands: GOL.30 5 PLIP interactions: 5 interactions with chain C Water bridges: C:R.231 Hydrophobic interactions: C:R.244, C:F.245 Hydrogen bonds: C:G.201, C:D.203, C:D.204

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

UDH.4: 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.5, GOL.14 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:D.235 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: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.15: 16 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, D.235, N.238 Ligands: MN.16, GOL.23 20 PLIP interactions: 20 interactions with chain B 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 Water bridges: B:R.74, B:K.164, B:K.164, 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.24: 17 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, R.231, H.232, R.234, D.235 Ligands: MN.25, GOL.30 22 PLIP interactions: 22 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.231, C:R.234, C:D.235, C:D.235 Water bridges: C:R.74, C:D.137, C:N.238, C:N.238 Salt bridges: C:R.76, C:K.164, C:H.229, C:H.232, C:H.232 pi-Stacking: C:F.111 pi-Cation interactions: C:R.76

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

MN.5: 4 residues within 4Å: Chain A: D.139, H.229, H.232 Ligands: UDH.4 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.16: 4 residues within 4Å: Chain B: D.139, H.229, H.232 Ligands: UDH.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.139, B:H.229, B:H.232, H2O.10 MN.25: 4 residues within 4Å: Chain C: D.139, H.229, H.232 Ligands: UDH.24 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.139, C:H.229, C:H.232, H2O.16

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

SO4.6: 4 residues within 4Å: Chain A: E.33, F.34, N.35, R.228 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain A: N.49, Y.56, P.58, R.59, D.60 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: Q.122, L.263, T.264, Y.265 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: F.152, R.156, R.219, P.220 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: S.257, D.258 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: F.152, S.153 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: H.232, S.233 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: F.207, S.216, I.217 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain B: E.33, F.34, N.35, R.228, R.231 Chain C: P.48, N.49 Ligand excluded by PLIP SO4.19: 5 residues within 4Å: Chain B: N.195, W.197, R.247, P.286, S.287 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: H.232, S.233 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: F.152, R.156, P.220 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: V.38, D.39, L.40, E.41, K.81 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: F.152, S.153 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: N.195, W.197, P.286, S.287 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain A: P.48, N.49 Chain C: E.33, F.34, N.35, R.228 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 9 residues within 4Å: Chain A: R.113, D.137, G.177, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG-GAL-NAG.1, UDH.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.113, A:G.177, A:W.199, A:G.200 Water bridges: A:G.198, A:G.200 GOL.23: 7 residues within 4Å: Chain B: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG-GAL-NAG.2, UDH.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.113, B:W.199, B:G.200 Water bridges: B:G.198, B:E.202 GOL.30: 9 residues within 4Å: Chain C: R.113, D.137, G.176, G.177, W.199, G.200, E.202 Ligands: BGC-GAL-NAG-GAL-NAG.3, UDH.24 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.113, C:G.177, C:W.199, C:G.200 Water bridges: C:Y.174

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Beta-1,4-galactosyltransferase 1

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