SMTL ID : 6yjs.2 (1 other biounit)

Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with biantennary pentasaccharide M592

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x MAN- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose

MAN-MAN-NAG-MAN-NAG.1: 15 residues within 4Å: Chain A: L.63, P.81, E.84, I.127, V.128, A.131, Q.132, L.151, D.152, S.153, F.154, W.175, F.324, K.328, P.329 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:P.81, A:K.328, A:E.84, A:L.151, A:D.152, A:D.152, A:S.153, A:K.328 Hydrophobic interactions: A:E.84 Water bridges: A:F.154, A:F.154

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

EDO.2: 7 residues within 4Å: Chain A: E.157, H.191, T.192, P.193, R.332, K.424, A.488 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.157, A:H.191, A:K.424 Water bridges: A:D.194 EDO.3: 12 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, P.375 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.371, A:K.372, A:E.374, A:E.374 Water bridges: A:A.307, A:A.307 EDO.4: 6 residues within 4Å: Chain A: F.291, Y.293, T.322, D.323, F.324 Ligands: SO4.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.323, A:F.324 EDO.5: 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:H.143, A:Q.145, A:C.146 EDO.7: 4 residues within 4Å: Chain A: T.65, S.107, L.108, A.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.65, A:L.108, A:A.109 EDO.8: 8 residues within 4Å: Chain A: Q.183, Q.397, D.398, F.399, W.406, P.407, E.435, S.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.183, A:S.437 EDO.9: 3 residues within 4Å: Chain A: Q.167, K.172, K.177 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.167, A:K.177 Water bridges: A:K.172 EDO.10: 3 residues within 4Å: Chain A: N.267, H.268, G.269 No protein-ligand interaction detected (PLIP)

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

NAG.6: 7 residues within 4Å: Chain A: R.219, N.221, H.244, T.245, Y.246, M.247, E.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.221

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

SO4.11: 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 SO4.12: 3 residues within 4Å: Chain A: K.56, R.103, G.117 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.56, A:G.117 Salt bridges: A:K.56, A:R.103 SO4.13: 3 residues within 4Å: Chain A: K.134, P.139, W.141 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.141 Water bridges: A:K.134, A:K.134 Salt bridges: A:K.134 SO4.14: 5 residues within 4Å: Chain A: N.321, T.322, D.323, F.324 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.323 Water bridges: A:K.317, A:N.321 SO4.15: 1 residues within 4Å: Chain A: R.347 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.347

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

Related Entries With Identical Sequence