Structure of PDB 5vcm Chain B

Receptor sequence
>5vcmB (length=358) Species: 9606 (Homo sapiens) [Search protein sequence]
AVPQPEADNLTLRYRSLVYQLNFDQTLRNVDKAGTWAPRELVLVVQVHNR
PEYLRLLLDSLRKAQGIDNVLVIFSHDFWSTEINQLIAGVNFCPVLQVFF
PFSIQLYPNEFPGSDPRDCPRDLPKNAALKLGCINAEYPDSFGHYREAKF
SQTKHHWWWKLHFVWERVKILRDYAGLILFLEEDHYLAPDFYHVFKKMWK
LKQQECPECDVLSLGTYSRSFYGMADKVDVKTWKSTEHNMGLALTRNAYQ
KLIECTDTFCTYDDYNWDWTLQYLTVSCLPKFWKVLVPQIPRIFHAGDCG
MHHKKTCRPSTQSAQIESLLMFPETLTISFTVVAISPPRKNGGWGDIRDH
ELCKSYRR
3D structure
PDB5vcm HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
ChainB
Resolution1.599 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 MN B D261 H374 D184 H295
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vcm, PDBe:5vcm, PDBj:5vcm
PDBsum5vcm
PubMed29666272
UniProtQ10469|MGAT2_HUMAN Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (Gene Name=MGAT2)

[Back to BioLiP]