SMTL ID : 7jhn.1

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP and trisaccharide GlcNAc-beta1-3Gal-beta1-4GlcNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 12 residues within 4Å: Chain A: C.69, E.70, R.88, D.91, F.92, Y.95, Y.101, Y.186, R.187, T.189, F.191, N.192 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.95, A:E.70, A:D.91, A:Y.101, A:R.187 Hydrophobic interactions: A:Y.101

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

NAG-GAL-NAG.2: 21 residues within 4Å: Chain A: K.122, F.190, L.193, D.218, I.249, H.250, N.251, A.252, H.255, Y.262, Y.273, Y.276, G.278, G.279, G.280, I.304, D.305, D.306, T.328, H.349 Ligands: UDP.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.122, A:K.122, A:D.218, A:G.280, A:D.306 Water bridges: A:P.303, A:D.305, A:H.349, A:H.255, A:Y.273, A:Y.276, A:Y.276

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 4 residues within 4Å: Chain A: N.67, C.69, N.100, Y.101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.101 Hydrogen bonds: A:N.67, A:N.100

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.220, H.349 Ligands: UDP.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.220, A:D.220, A:H.349, H2O.1, H2O.3

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

UDP.5: 17 residues within 4Å: Chain A: K.122, S.123, L.124, H.127, D.188, T.189, F.190, L.193, K.196, D.218, D.219, D.220, K.261, Y.262, H.349 Ligands: NAG-GAL-NAG.2, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.124 Hydrogen bonds: A:H.127, A:D.188, A:K.196, A:D.218, A:D.218, A:D.219, A:D.219, A:Y.262, A:Y.262 Water bridges: A:K.261 Salt bridges: A:K.261, A:K.261, A:H.349

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 2 residues within 4Å: Chain A: R.151, H.178 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hao, Y. et al., Structures and mechanism of human glycosyltransferase beta 1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), an important player in immune homeostasis. J.Biol.Chem. (2020)

Release Date

2020-11-18

Peptides

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2

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