SMTL ID : 6yjv.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, in complex with UDP-2-deoxy-2-fluoroglucose and biantennary pentasaccharide M592

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-NAG.1: 16 residues within 4Å: Chain A: L.63, F.70, I.72, P.81, E.84, I.127, V.128, L.151, D.152, S.153, F.154, W.175, F.324, K.328, P.329 Ligands: U2F.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.328, A:E.84, A:L.151, A:D.152, A:D.152, A:S.153, A:K.328 Water bridges: A:E.84, A:E.84, A:S.153, A:F.154, A:F.154 Hydrophobic interactions: A:E.84

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

EDO.2: 6 residues within 4Å: Chain A: L.2, A.3, E.4, R.6, R.54, G.99 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.4, A:G.99

1 x U2F: URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE(Non-covalent)

U2F.3: 28 residues within 4Å: Chain A: W.24, P.81, L.82, G.83, E.84, V.86, S.153, F.154, M.188, Y.226, K.228, T.252, I.270, L.271, G.273, L.276, F.291, P.292, Y.293, E.294, G.295, P.296, A.297, P.298, E.300, F.324 Ligands: MAN-NAG.1, MAN-NAG.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.276 Hydrogen bonds: A:L.82, A:G.83, A:S.153, A:S.153, A:Y.226, A:Y.226, A:K.228, A:T.252, A:L.271, A:L.271, A:Y.293, A:A.297, A:E.300 Water bridges: A:R.28, A:E.300 Salt bridges: A:K.228, A:K.228

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

SO4.4: 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 SO4.5: 5 residues within 4Å: Chain A: M.16, K.17, K.18, R.23, R.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.18 Salt bridges: A:R.23, A:R.26 SO4.6: 1 residues within 4Å: Chain A: R.347 No protein-ligand interaction detected (PLIP)

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

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

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