Structure of PDB 5vcs Chain A

Receptor sequence
>5vcsA (length=354) Species: 9606 (Homo sapiens) [Search protein sequence]
VPQPEADNLTLRYRSLVYQLNFDQTLRNVDKAGTWAPRELVLVVQVHNRP
EYLRLLLDSLRKAQGIDNVLVIFSHDFWSTEINQLIAGVNFCPVLQVFFP
FSIQLYPNEFPGSDPRDCPRDLPKNAALKLGCINAEYPDSFGHYREAKFS
QTKHHWWWKLHFVWERVKILRDYAGLILFLEEDHYLAPDFYHVFKKMWKL
KQQECPECDVLSLGTYSASRSFYGMADKVDVKTWKSTEHNMGLALTRNAY
QKLIECTDTFCTYDDYNWDWTLQYLTVSCLPKFWKVLVPQIPRIFHAGRP
STQSAQIESLLNNNKQYMFPETLTISEVVAISPPRKNGGWGDIRDHELCK
SYRR
3D structure
PDB5vcs HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
ChainA
Resolution2.799 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.4.1.143: alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 BMA A Y344 N345 W348 N428 Y266 N267 W270 N337
BS02 MAN A T315 N318 D347 W348 T237 N240 D269 W270
Gene Ontology
Molecular Function
GO:0008455 alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0030145 manganese ion binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006486 protein glycosylation
GO:0006487 protein N-linked glycosylation
GO:0009312 oligosaccharide biosynthetic process
GO:0018279 protein N-linked glycosylation via asparagine
GO:0019082 viral protein processing
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vcs, PDBe:5vcs, PDBj:5vcs
PDBsum5vcs
PubMed29666272
UniProtQ10469|MGAT2_HUMAN Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (Gene Name=MGAT2)

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