Structure of PDB 5vcm Chain A Binding Site BS02

Receptor Information
>5vcm Chain A (length=351) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLTLRYRSLVYQLNFDQTLRNVDWAPRELVLVVQVHNRPEYLRLLLDSLR
KAQGIDNVLVIFSHDFWSTEINQLIAGVNFCPVLQVFFPFSIQLYPNEFP
GSDPRDCPRDLPKNAALKLGCINAEYPDSFGHYREAKFSQTKHHWWWKLH
FVWERVKILRDYAGLILFLEEDHYLAPDFYHVFKKMWKLKQQECPECDVL
SLGTYSSRSFYGMADKVDVKTWKSTEHNMGLALTRNAYQKLIECTDTFCT
YDDYNWDWTLQYLTVSCLPKFWKVLVPQIPRIFHAGDCGCRPSTQSAQIE
SLLNNNKQYMFPETLTISEKFTVVAISPPRKNGGWGDIRDHELCKSYRRL
Q
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain5vcm Chain A Residue 502 [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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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)		Q123 H125 R127 D154 Q229 T230 E259 E260 D261 H374
Binding residue
(residue number reindexed from 1)		Q34 H36 R38 D65 Q140 T141 E170 E171 D172 H284
Annotation score3
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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