SMTL ID : 6yjq.2 (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

5 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.305, A:Q.371, A:E.374 Water bridges: A:G.305, A:A.307, A:A.307 EDO.2: 5 residues within 4Å: Chain A: V.142, H.143, Y.144, Q.145, C.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.142, A:Q.145, A:C.146 EDO.3: 8 residues within 4Å: Chain A: L.82, G.83, 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 EDO.4: 6 residues within 4Å: Chain A: F.291, Y.293, T.322, D.323, F.324 Ligands: SO4.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.293, A:D.323, A:F.324 EDO.6: 10 residues within 4Å: Chain A: F.160, H.171, T.173, S.319, K.320, F.325, G.327, K.328, T.330, L.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.319, A:S.319, A:G.327

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

NAG.5: 6 residues within 4Å: Chain A: R.219, N.221, H.244, Y.246, M.247, E.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.221

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

SO4.7: 4 residues within 4Å: Chain A: K.17, K.18, R.23, R.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.18 Salt bridges: A:K.17, A:R.23, A:R.26 SO4.8: 2 residues within 4Å: Chain A: K.56, R.103 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.56, A:R.103 SO4.9: 1 residues within 4Å: Chain A: N.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 SO4.10: 4 residues within 4Å: Chain A: T.65, K.66, S.107, L.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.66, A:L.108 Water bridges: A:A.109 SO4.11: 4 residues within 4Å: Chain A: N.321, T.322, D.323 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.323 Water bridges: A:K.317 SO4.12: 1 residues within 4Å: Chain A: K.317 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.317 Salt bridges: A:K.317

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
BBB

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

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