SMTL ID : 4eeo.4 (3 other biounits)

Crystal structure of human M340H-beta-1,4-galactosyltransferase-1 (M340H-B4GAL-T1) in complex with GLCNAC-BETA1,6-GlcNAc-ALPHA-benzyl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x BBV- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-benzyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside(Non-covalent)

BBV-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.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.204, A:F.245, A:I.248, A:I.248, A:F.245 Hydrogen bonds: A:Y.171, A:G.201, A:D.203, A:D.204, A:D.204, A:R.244 BBV-NAG.2: 12 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, I.248 Ligands: GOL.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.204, B:F.245, B:I.248, B:I.248, B:F.245 Hydrogen bonds: B:G.201, B:D.203, B:D.204, B:D.204, B:R.244 Water bridges: B:Y.174 BBV-NAG.3: 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.23 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.248, 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 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.10 18 PLIP interactions: 18 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:W.199, A:D.235, A:D.235 Water bridges: A:R.74, 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.11: 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.12, GOL.18 18 PLIP interactions: 18 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 Water bridges: B:D.137, B:D.137, 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.19: 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.20, GOL.23 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:P.72, C:R.74, C:R.74, C:R.76, C:V.138, C:D.139, C:D.139, C:D.235, C:D.235 Water bridges: C:D.137, C:D.137 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

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

MN.5: 4 residues within 4Å: Chain A: D.139, H.229, H.232 Ligands: UDP.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.2 MN.12: 4 residues within 4Å: Chain B: D.139, H.229, H.232 Ligands: UDP.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.139, B:H.229, B:H.232 MN.20: 4 residues within 4Å: Chain C: D.139, H.229, H.232 Ligands: UDP.19 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

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

SO4.6: 4 residues within 4Å: Chain A: E.33, F.34, N.35, R.228 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:N.49, B:N.49 Hydrogen bonds: A:F.34 Salt bridges: A:R.228 SO4.7: 5 residues within 4Å: Chain A: N.49, Y.56, P.58, R.59, D.60 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.56, A:R.59, A:D.60, A:D.60 Water bridges: A:N.49 Salt bridges: A:R.59 SO4.8: 2 residues within 4Å: Chain A: T.264, Y.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.122, A:Y.265 Water bridges: A:Y.265 SO4.9: 3 residues within 4Å: Chain A: S.257, D.258, S.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.257, A:D.258 SO4.13: 4 residues within 4Å: Chain B: N.49, Y.56, P.58, R.59 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.49, B:Y.56, B:R.59 Salt bridges: B:R.59 Water bridges: A:R.228 SO4.14: 5 residues within 4Å: Chain B: N.195, W.197, R.247, P.286, S.287 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.195, B:S.287, B:S.287, B:S.287 Salt bridges: B:R.247 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: E.33, F.34, N.35, R.228, R.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.34 Salt bridges: B:R.228, B:R.231 SO4.17: 3 residues within 4Å: Chain B: F.152, R.156, P.220 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.156 Salt bridges: B:R.156 SO4.21: 5 residues within 4Å: Chain C: N.49, Y.56, P.58, R.59, D.60 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.49, C:Y.56, C:R.59, C:D.60 Water bridges: C:D.60, C:D.60 Salt bridges: C:R.59 SO4.22: 5 residues within 4Å: Chain A: N.49 Chain C: E.33, F.34, N.35, R.228 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:F.34, C:N.35, A:N.49 Salt bridges: C:R.228

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: R.113, W.199, G.200, E.202, D.203 Ligands: BBV-NAG.1, UDP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.199, A:G.200, A:D.203 Water bridges: A:G.198, A:E.202 GOL.18: 7 residues within 4Å: Chain B: R.113, W.199, G.200, E.202, D.203 Ligands: BBV-NAG.2, UDP.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.113, B:W.199, B:G.200 Water bridges: B:G.198, B:E.202, B:N.238 GOL.23: 7 residues within 4Å: Chain C: R.113, W.199, G.200, E.202, D.203 Ligands: BBV-NAG.3, UDP.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.113, C:W.199, C:G.200

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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