SMTL ID : 6yjt.1 (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 UDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 22 residues within 4Å: Chain A: W.24, G.80, P.81, L.82, G.83, V.86, Y.226, K.228, T.252, I.270, L.271, S.272, G.273, L.276, Q.277, P.292, G.295, P.296, A.297, P.298, E.300 Ligands: EDO.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.82, A:G.83, A:Y.226, A:K.228, A:T.252, A:L.271, A:L.271, A:A.297, A:E.300, A:E.300 Salt bridges: A:K.228, A:K.228

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

EDO.2: 9 residues within 4Å: Chain A: G.305, C.306, A.307, P.348, H.349, Q.371, K.372, I.373, E.374 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.372, A:E.374, A:E.374 Water bridges: A:A.307 EDO.3: 6 residues within 4Å: Chain A: H.244, E.248, V.249, Y.264, K.266 Ligands: NAG.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.244 Water bridges: A:Y.264 EDO.4: 5 residues within 4Å: Chain A: K.134, P.174, G.176, K.177, W.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.134, A:G.176 Water bridges: A:W.178 EDO.5: 10 residues within 4Å: Chain A: G.83, F.154, M.188, Y.226, P.292, Y.293, E.294, G.295, P.296 Ligands: UDP.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.83, A:G.83

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, Y.246, M.247, E.248 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.221

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

SO4.7: 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

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

Related Entries With Identical Sequence