Structure of PDB 3otk Chain D Binding Site BS01

Receptor Information
>3otk Chain D (length=364) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NVNCTKILQGDPEEIQKVKLEILTVPRWTPHDYINMTRDCASFIRTRKYI
VEPLTKEEVGFPIAYSIVVHHKIEMLDRLLRAIYMPQNFYCIHVDRKAEE
SFLAAVQGIASCFDNVFVASQLESVVYASWTRVKADLNCMKDLYRMNANW
KYLINLSGMDFPIKTNLEIVRKLKCSTGENNLETEKMPPNKEERWKKRYA
VVDGKLTNTGIVKAPPPLKTPLFSGSAYFVVTREYVGYVLENENIQKLME
WAQDTYSPDEFLWATIQRIPEVPGSFPSSNKYDLSDMNAIARFVKWQYFE
GDVSNGAPYPPCSGVHVRSVCVFGAGDLSWMLRQHHLFANKFDMDVDPFA
IQCLDEHLRRKALE
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 chain3otk Chain D Residue 601 [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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PDB3otk Structural and mechanistic characterization of leukocyte-type core 2 beta 1,6-N-acetylglucosaminyltransferase: a metal-ion-independent GT-A glycosyltransferase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		V128 H130 D155 V185 Y187 S217 R378
Binding residue
(residue number reindexed from 1)		V68 H70 D95 V125 Y127 S157 R318
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.1.102: beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N- acetylglucosaminyltransferase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003829 beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
GO:0016757 glycosyltransferase activity
Biological Process
GO:0006486 protein glycosylation
GO:0009101 glycoprotein biosynthetic process
GO:0016268 O-glycan processing, core 2
GO:0032868 response to insulin
GO:0048729 tissue morphogenesis
GO:0050901 leukocyte tethering or rolling
GO:0060352 cell adhesion molecule production
GO:0060993 kidney morphogenesis
GO:1903238 positive regulation of leukocyte tethering or rolling
Cellular Component
GO:0000139 Golgi membrane
GO:0005615 extracellular space
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0016020 membrane
GO:0031985 Golgi cisterna

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3otk, PDBe:3otk, PDBj:3otk
PDBsum3otk
PubMed22056345
UniProtQ09324|GCNT1_MOUSE Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (Gene Name=Gcnt1)

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