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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.233, H.346 Ligands: UDP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.233, A:H.346, H2O.2, H2O.3

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

UDP.2: 13 residues within 4Å: Chain A: Q.95, V.96, H.97, R.99, D.126, Q.201, T.202, H.205, E.231, E.232, D.233, H.346 Ligands: MN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.97 Hydrogen bonds: A:Q.95, A:Q.95, A:H.97, A:D.126, A:Q.201, A:E.232 Water bridges: A:R.99, A:R.99, A:E.232, A:E.232 Salt bridges: A:R.99, A:H.346

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

DMS.3: 3 residues within 4Å: Chain A: A.113, Q.114, G.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.114, A:G.115 Water bridges: A:I.116 Salt bridges: A:D.117 DMS.4: 6 residues within 4Å: Chain A: K.246, K.249, L.250, Q.253, T.382, L.383 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.383 DMS.6: 1 residues within 4Å: Chain A: N.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118 Water bridges: A:K.245

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 10 residues within 4Å: Chain A: V.67, H.125, D.126, F.127, W.128, F.148, F.149, S.152, Q.154, L.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.128, A:F.149, A:S.152, A:Q.154

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
A

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

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