Structure of PDB 5vcm Chain B Binding Site BS01

Receptor Information
>5vcm Chain B (length=358) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVPQPEADNLTLRYRSLVYQLNFDQTLRNVDKAGTWAPRELVLVVQVHNR
PEYLRLLLDSLRKAQGIDNVLVIFSHDFWSTEINQLIAGVNFCPVLQVFF
PFSIQLYPNEFPGSDPRDCPRDLPKNAALKLGCINAEYPDSFGHYREAKF
SQTKHHWWWKLHFVWERVKILRDYAGLILFLEEDHYLAPDFYHVFKKMWK
LKQQECPECDVLSLGTYSRSFYGMADKVDVKTWKSTEHNMGLALTRNAYQ
KLIECTDTFCTYDDYNWDWTLQYLTVSCLPKFWKVLVPQIPRIFHAGDCG
MHHKKTCRPSTQSAQIESLLMFPETLTISFTVVAISPPRKNGGWGDIRDH
ELCKSYRR
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain5vcm Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vcm HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
Resolution1.599 Å
Binding residue
(original residue number in PDB)		D261 H374
Binding residue
(residue number reindexed from 1)		D184 H295
Annotation score1
Enzymatic activity
Enzyme Commision number 2.4.1.143: alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase.
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:5vcm, PDBe:5vcm, PDBj:5vcm
PDBsum5vcm
PubMed29666272
UniProtQ10469|MGAT2_HUMAN Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (Gene Name=MGAT2)

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