SMTL ID : 6yjq.1 (1 other biounit)

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

EDO.1: 11 residues within 4Å: Chain A: K.284, G.305, C.306, A.307, P.348, H.349, I.368, Q.371, K.372, I.373, E.374 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.371, A:K.372, A:E.374 Water bridges: A:A.307 EDO.2: 9 residues within 4Å: Chain A: Y.340, F.344, P.378, E.380, F.503, K.505, G.506, Q.507, V.508 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.380, A:G.506 EDO.3: 4 residues within 4Å: Chain A: H.244, E.248, Y.264, K.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.244 Water bridges: A:Y.264

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

SO4.4: 3 residues within 4Å: Chain A: K.56, R.103, G.117 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.117, A:G.118 Salt bridges: A:K.56, A:R.103 SO4.5: 2 residues within 4Å: Chain A: N.48, K.396 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 SO4.6: 4 residues within 4Å: Chain A: L.27, R.31, G.273, R.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.274 Salt bridges: A:R.31, A:R.274 SO4.7: 6 residues within 4Å: Chain A: Y.226, P.292, G.295, P.296, A.297, P.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.226, A:Y.226, A:A.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Darby, J.F. et al., Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V. Acs Catalysis (2020)

Release Date

2020-08-05

Peptides

Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A,Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A

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