Structure of PDB 7y4i Chain A Binding Site BS01

Receptor Information
>7y4i Chain A (length=822) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FSNGSRSSSSSAGVLSPSNDTLSYANILRARNKFADALALYEAMLEKDSK
NVEAHIGKGICLQTQNKGNLAFDCFSEAIRLDPHNACALTHCGILHKEEG
RLVEAAESYQKALMADASYKPAAECLAIVLTDLGTSLKLAGNTQEGIQKY
YEALKIDPHYAPAYYNLGVVYSEMMQYDNALSCYEKAALERPMYAEAYCN
MGVIYKNRGDLEMAITCYERCLAVSPNFEIAKNNMAIALTDLGTKVKLEG
DVTQGVAYYKKALYYNWHYADAMYNLGVAYGEMLKFDMAIVFYELAFHFN
PHCAEACNNLGVLYKDRDNLDKAVECYQMALSIKPNFAQSLNNLGVVYTV
QGKMDAAASMIEKAILANPTYAEAFNNLGVLYRDAGNITMAIDAYEECLK
IDPDSRNAGQNRLLAMNYINEGLDDKLFEAHRDWGWRFTRLHPQYTSWDN
LKDPERPITIGYISPDFFTHSVSYFIEAPLTHHDYTKYKVVVYSAVVKAD
AKTYRFRDKVLKKGGVWKDIYGIDEKKIASMVREDKIDILVELTGHTANN
KLGTMACRPAPVQVTWIGYPNTTGLPTVDYRITDSLADPPDTKQKQVEEL
VRLPDCFLCYTPSPEAGPVSPTPALSNGFVTFGSFNNLAKITPKVLQVWA
RILCAVPNSRLVVKCKPFCCDSIRQRFLTTLEQLGLESKRVDLLPLILFN
HDHMQAYSLMDISLDTFPYAGTTTTCESLYMGVPCVTMAGSVHAHNVGVS
LLTKVGLGHLVAKNEDEYVQLSVDLASDVTALSKLRMSLRDLMAGSPVCN
GPSFAVGLESAYRNMWKKYCKG
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain7y4i Chain A Residue 1901 [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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PDB7y4i Structural insights into mechanism and specificity of the plant protein O-fucosyltransferase SPINDLY.
Resolution2.85 Å
Binding residue
(original residue number in PDB)		S496 Y499 K665 L721 I722 L723 H728 G746 T747 T748 T749 E752
Binding residue
(residue number reindexed from 1)		S471 Y474 K640 L696 I697 L698 H703 G721 T722 T723 T724 E727
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.221: peptide-O-fucosyltransferase.
2.4.1.255: protein O-GlcNAc transferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016262 protein N-acetylglucosaminyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0046922 peptide-O-fucosyltransferase activity
GO:0097363 protein O-acetylglucosaminyltransferase activity
Biological Process
GO:0006486 protein glycosylation
GO:0009736 cytokinin-activated signaling pathway
GO:0009740 gibberellic acid mediated signaling pathway
GO:0009908 flower development
GO:0009938 negative regulation of gibberellic acid mediated signaling pathway
GO:0030154 cell differentiation
GO:0036066 protein O-linked fucosylation
GO:0048511 rhythmic process
GO:2000377 regulation of reactive oxygen species metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7y4i, PDBe:7y4i, PDBj:7y4i
PDBsum7y4i
PubMed36456586
UniProtQ96301|SPY_ARATH Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY (Gene Name=SPY)

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