- PDB-8ce3: Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta... -
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Basic information
Entry
Database: PDB / ID: 8ce3
Title
Crystal structure of MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with 3D fragment 2548
Components
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A
Keywords
CARBOHYDRATE / Glycosyltransferase / fragment
Function / homology
Function and homology information
alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein ...alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase / alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity / N-Glycan antennae elongation / positive regulation of receptor signaling pathway via STAT / negative regulation of protein tyrosine phosphatase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / protein phosphatase inhibitor activity / manganese ion binding / Maturation of spike protein / viral protein processing / positive regulation of cell migration / Golgi membrane / Golgi apparatus / extracellular exosome / membrane Similarity search - Function
Glycosyltransferase family 18 / Domain of unknown function DUF4525 / Glycosyltransferase family 18 / Domain of unknown function (DUF4525) Similarity search - Domain/homology
A: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A B: Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A hetero molecules
Evidence: gel filtration, elutes as a single peak at expected retention time for a monomer
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
5390 Å2
ΔGint
-100 kcal/mol
Surface area
41820 Å2
Unit cell
Length a, b, c (Å)
46.860, 68.540, 91.310
Angle α, β, γ (deg.)
107.300, 92.160, 107.050
Int Tables number
1
Space group name H-M
P1
Noncrystallographic symmetry (NCS)
NCS domain:
ID
Ens-ID
Details
1
1
A
2
1
A
NCS domain segments:
Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 214 - 728 / Label seq-ID: 1 - 515
Dom-ID
1
2
NCS ensembles : (Details: Local NCS retraints between domains: 1 2)
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Components
#1: Protein
Alpha-1,6-mannosylglycoprotein6-beta-N-acetylglucosaminyltransferaseA / Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase V / GlcNAc-T V / GNT-V / Mannoside ...Alpha-mannoside beta-1 / 6-N-acetylglucosaminyltransferase V / GlcNAc-T V / GNT-V / Mannoside acetylglucosaminyltransferase 5 / N-acetylglucosaminyl-transferase V
Mass: 58996.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MGAT5, GGNT5 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q09328, alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase
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