Structure of PDB 5vcs Chain A Binding Site BS01

Receptor Information
>5vcs Chain A (length=354) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPQPEADNLTLRYRSLVYQLNFDQTLRNVDKAGTWAPRELVLVVQVHNRP
EYLRLLLDSLRKAQGIDNVLVIFSHDFWSTEINQLIAGVNFCPVLQVFFP
FSIQLYPNEFPGSDPRDCPRDLPKNAALKLGCINAEYPDSFGHYREAKFS
QTKHHWWWKLHFVWERVKILRDYAGLILFLEEDHYLAPDFYHVFKKMWKL
KQQECPECDVLSLGTYSASRSFYGMADKVDVKTWKSTEHNMGLALTRNAY
QKLIECTDTFCTYDDYNWDWTLQYLTVSCLPKFWKVLVPQIPRIFHAGRP
STQSAQIESLLNNNKQYMFPETLTISEVVAISPPRKNGGWGDIRDHELCK
SYRR
Ligand information
Ligand IDBMA
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6-/m1/s1
InChIKeyWQZGKKKJIJFFOK-RWOPYEJCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O)O)O)O)O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namebeta-D-mannopyranose;
beta-D-mannose;
D-mannose;
mannose
ChEMBL
DrugBank
ZINCZINC000003830679
PDB chain5vcs Chain C Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5vcs HumanN-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
Resolution2.799 Å
Binding residue
(original residue number in PDB)		Y344 N345 W348 N428
Binding residue
(residue number reindexed from 1)		Y266 N267 W270 N337
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
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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