SMTL ID : 4eea.4 (4 other biounits)

Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with GLCNAC-BETA1,6-Gal-Beta1,4-Glc-BETA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

BGC-GAL-NAG.1: 12 residues within 4Å: Chain A: K.164, F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: GOL.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.164, A:R.244, A:R.244, A:Y.171, A:G.201, A:D.203, A:D.204 Water bridges: A:K.164, A:W.199, A:K.164 Salt bridges: A:K.164 Hydrophobic interactions: A:R.244, A:F.245 BGC-GAL-NAG.2: 13 residues within 4Å: Chain B: K.164, F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: UDP.13, GOL.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.244, B:R.244, B:Y.171, B:G.201, B:D.203, B:D.204, B:D.204, B:R.244 Hydrophobic interactions: B:R.244, B:F.245 Water bridges: B:Y.174 BGC-GAL-NAG.3: 12 residues within 4Å: Chain C: K.164, F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: GOL.27 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.164, C:R.244, C:G.201, C:D.203, C:D.204 Hydrophobic interactions: C:F.245 Water bridges: C:Y.174 BGC-GAL-NAG.34: 12 residues within 4Å: Chain D: K.164, F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: GOL.39 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.164, D:R.244, D:R.244, D:G.201, D:D.203, D:D.204 Water bridges: D:K.164, D:W.199, D:K.164, D:Y.174 Salt bridges: D:K.164 Hydrophobic interactions: D:R.244, D:F.245 BGC-GAL-NAG.35: 13 residues within 4Å: Chain E: K.164, F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: UDP.46, GOL.48 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.244, E:R.244, E:G.201, E:D.203, E:D.204, E:D.204, E:R.244 Hydrophobic interactions: E:R.244, E:F.245 BGC-GAL-NAG.36: 12 residues within 4Å: Chain F: K.164, F.165, Y.171, Y.174, W.199, G.200, G.201, D.203, D.204, R.244, F.245 Ligands: GOL.60 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.164, F:R.244, F:Y.171, F:G.201, F:D.203, F:D.204 Hydrophobic interactions: F:F.245

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

UDP.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.6 21 PLIP interactions: 21 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: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 UDP.13: 17 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: BGC-GAL-NAG.2, MN.14, GOL.15 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:W.199, B:D.235, B:D.235 Water bridges: B:R.74, B:D.137, B:N.238, B:N.238 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 UDP.25: 16 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, D.235, N.238 Ligands: MN.26, GOL.27 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:P.72, C:R.74, C:R.74, C:R.76, C:V.138, C:D.139 Water bridges: C:D.137, C:D.137, C:N.238 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 UDP.37: 16 residues within 4Å: Chain D: 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.38, GOL.39 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:P.72, D:R.74, D:R.74, D:R.76, D:D.137, D:V.138, D:D.139, D:D.235 Water bridges: D:R.74, D:R.74, D:K.164, D:K.164, D:N.238, D:N.238 Salt bridges: D:R.76, D:K.164, D:H.229, D:H.232, D:H.232 pi-Stacking: D:F.111 pi-Cation interactions: D:R.76 UDP.46: 17 residues within 4Å: Chain E: 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: BGC-GAL-NAG.35, MN.47, GOL.48 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:P.72, E:R.74, E:R.74, E:R.76, E:V.138, E:D.139, E:W.199, E:D.235 Water bridges: E:R.74, E:D.235, E:D.235, E:N.238, E:N.238 Salt bridges: E:R.76, E:K.164, E:H.229, E:H.232, E:H.232 pi-Stacking: E:F.111 pi-Cation interactions: E:R.76 UDP.58: 16 residues within 4Å: Chain F: 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.59, GOL.60 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:P.72, F:R.74, F:R.74, F:R.76, F:V.138, F:D.139 Water bridges: F:N.238 Salt bridges: F:R.76, F:K.164, F:H.232, F:H.232 pi-Stacking: F:F.111 pi-Cation interactions: F:R.76

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

MN.5: 4 residues within 4Å: Chain A: D.139, H.229, H.232 Ligands: UDP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.139, A:H.229, A:H.232 MN.14: 4 residues within 4Å: Chain B: D.139, H.229, H.232 Ligands: UDP.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.139, B:H.229, B:H.232 MN.26: 4 residues within 4Å: Chain C: D.139, H.229, H.232 Ligands: UDP.25 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.139, C:H.229, C:H.232, H2O.25 MN.38: 4 residues within 4Å: Chain D: D.139, H.229, H.232 Ligands: UDP.37 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.139, D:H.229, D:H.232 MN.47: 4 residues within 4Å: Chain E: D.139, H.229, H.232 Ligands: UDP.46 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.139, E:H.229, E:H.232 MN.59: 4 residues within 4Å: Chain F: D.139, H.229, H.232 Ligands: UDP.58 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.139, F:H.229, F:H.232, H2O.53

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.1, UDP.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.200, A:E.202, A:D.203 GOL.15: 7 residues within 4Å: Chain B: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.2, UDP.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.200, B:E.202 Water bridges: B:N.238 GOL.16: 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.27: 7 residues within 4Å: Chain C: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.3, UDP.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.199, C:G.200, C:D.203 GOL.39: 7 residues within 4Å: Chain D: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.34, UDP.37 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.200, D:E.202, D:D.203 GOL.48: 7 residues within 4Å: Chain E: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.35, UDP.46 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.200, E:E.202 Water bridges: E:E.202, E:N.238 GOL.49: 4 residues within 4Å: Chain E: F.73, R.74, N.75, N.104 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.75, E:N.75, E:N.104 GOL.60: 7 residues within 4Å: Chain F: R.113, W.199, G.200, E.202, D.203 Ligands: BGC-GAL-NAG.36, UDP.58 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:W.199, F:G.200, F:D.203

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

SO4.7: 4 residues within 4Å: Chain A: E.33, F.34, N.35, R.228 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: F.152, R.156 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: H.232, S.233 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: K.51, M.52 Ligand excluded by PLIP SO4.12: 8 residues within 4Å: Chain A: F.207, V.211, S.216, I.217 Chain E: F.207, M.215, S.216, I.217 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain B: E.33, F.34, N.35, R.228, R.231 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain B: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: F.152, R.156, P.220 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: Q.122, T.264, Y.265 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain B: M.36, P.37, V.38, D.39, Y.85 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain B: N.195, W.197, R.247, P.286, S.287 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain B: V.38, D.39, L.40, E.41, K.81 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain C: E.123, K.126, Y.265, Q.266, V.267 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain A: N.49 Chain C: E.33, F.34, N.35, R.228 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain C: H.232, S.233 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain C: F.152, R.156, P.220 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: R.150, F.152, S.153 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain D: E.33, F.34, N.35, R.228 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain D: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain D: F.152, R.156 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain D: H.232, S.233 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain D: K.51, M.52 Ligand excluded by PLIP SO4.45: 8 residues within 4Å: Chain B: F.207, M.215, S.216, I.217 Chain D: F.207, V.211, S.216, I.217 Ligand excluded by PLIP SO4.50: 5 residues within 4Å: Chain E: E.33, F.34, N.35, R.228, R.231 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain E: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain E: F.152, R.156, P.220 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain E: H.232, S.233 Ligand excluded by PLIP SO4.54: 3 residues within 4Å: Chain E: Q.122, T.264, Y.265 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain E: M.36, P.37, V.38, D.39, Y.85 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain E: N.195, W.197, R.247, P.286, S.287 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain E: V.38, D.39, L.40, E.41, K.81 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain F: N.49, Y.56, P.58, R.59 Ligand excluded by PLIP SO4.62: 5 residues within 4Å: Chain F: E.123, K.126, Y.265, Q.266, V.267 Ligand excluded by PLIP SO4.63: 5 residues within 4Å: Chain D: N.49 Chain F: E.33, F.34, N.35, R.228 Ligand excluded by PLIP SO4.64: 2 residues within 4Å: Chain F: H.232, S.233 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain F: F.152, R.156, P.220 Ligand excluded by PLIP SO4.66: 3 residues within 4Å: Chain F: R.150, F.152, S.153 Ligand excluded by PLIP

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Beta-1,4-galactosyltransferase 1

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