SMTL ID : 6yjv.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, 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- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose

MAN-MAN-NAG-MAN.1: 16 residues within 4Å: Chain A: L.63, G.69, F.70, I.72, P.81, E.84, I.127, L.151, D.152, S.153, F.154, W.175, F.324, K.328, P.329 Ligands: U2F.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.70, A:I.72, A:E.84 Hydrogen bonds: A:E.84, A:E.84, A:L.151, A:D.152, A:S.153, A:K.328 Water bridges: A:S.153, A:F.154, A:F.154

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

EDO.2: 9 residues within 4Å: Chain A: M.32, A.35, V.201, V.202, E.203, Q.204, H.205, M.377, C.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.202, A:Q.204, A:Q.204

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

U2F.3: 23 residues within 4Å: Chain A: W.24, G.79, G.80, P.81, L.82, G.83, V.86, Y.226, K.228, V.229, F.232, T.252, L.276, F.291, P.292, G.295, P.296, A.297, P.298, E.300, F.324 Ligands: MAN-MAN-NAG-MAN.1, MAN-MAN-NAG-MAN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.82, A:G.83, A:Y.226, A:K.228, A:A.297, A:E.300 Water bridges: A:E.84 Salt bridges: A:K.228, A:K.228, A:K.228

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

SO4.4: 3 residues within 4Å: Chain A: K.56, R.103, G.117 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.56, A:R.103 SO4.5: 5 residues within 4Å: Chain A: H.244, E.248, V.249, Y.264, K.266 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.244 Salt bridges: A:H.244, A:K.266 SO4.6: 2 residues within 4Å: Chain A: R.31, R.274 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.274

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
AAA

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

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