SMTL ID : 5vcm.2 (1 other biounit)

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound UDP and Manganese

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MN.1: 2 residues within 4Å: Chain A: D.233, H.346 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.233, A:H.346, H2O.2, H2O.2, H2O.5, H2O.8

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

NAG.2: 4 residues within 4Å: Chain A: N.58, T.60, L.61, R.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.58, A:L.61, A:R.64 Water bridges: A:R.64, A:R.64

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: R.398, K.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.399 DMS.4: 5 residues within 4Å: Chain A: E.305, C.306, D.308, T.309, C.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.308, A:T.309 DMS.5: 3 residues within 4Å: Chain A: F.199, Y.316, N.317 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.316 DMS.6: 2 residues within 4Å: Chain A: Q.114, G.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.115 Water bridges: A:I.116 Salt bridges: A:D.117 DMS.7: 3 residues within 4Å: Chain A: S.129, T.130, E.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadirvelraj, R. et al., HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-04-11

Peptides

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase

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