SMTL ID : 7jhi.1 (3 other biounits)

Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 iodide-derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 12 residues within 4Å: Chain A: C.83, P.85, R.102, D.105, F.106, Y.109, Y.115, Y.200, R.201, T.203, F.205, N.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.109, A:D.105, A:R.201 Hydrophobic interactions: A:Y.115

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

NAG.2: 5 residues within 4Å: Chain A: N.81, C.83, C.112, N.114, Y.115 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.115

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.232, D.234, H.363 Ligands: UDP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.234, A:D.234, A:H.363, H2O.1

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

UDP.4: 16 residues within 4Å: Chain A: K.136, S.137, L.138, H.141, D.202, T.203, F.204, L.207, K.210, D.232, D.233, D.234, K.275, Y.276, H.363 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.202, A:D.202, A:D.233, A:D.233, A:Y.276, A:Y.276 Water bridges: A:D.234, A:D.234, A:K.275, A:H.363 Salt bridges: A:K.275, A:K.275, A:H.363

11 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 2 residues within 4Å: Chain A: Q.56, R.111 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: R.102 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: L.117, R.216 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: T.172 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: K.128, F.130 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: N.238, V.357, L.377 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: Y.245 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: P.173, R.201 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: L.274, Y.276 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: H.141, A.143, R.144 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: H.264 Ligand excluded by PLIP

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

CL.16: 2 residues within 4Å: Chain A: S.250, K.253 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: E.346, N.349 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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