Structure of PDB 3zy3 Chain B Binding Site BS01

Receptor Information
>3zy3 Chain B (length=347) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDPNGYIVFCPCMGRFGNQVDQFLGVLAFAKALDRTLVLPNFIEFKPETK
MIPFEFLFQVGTVAKYTRVVTMQEFTKKIMPTVWPPEKRKAFCWTPRQAI
YEPGCHSKEGNPFGPYWDQIDVSFVGDEYFGDIPGGFDLNQMGSRKKWLE
KFPSEEYPVLAFSSAPAPFPSKGKVWSIQKYLRWSSRITEQAKKFISANL
AKPFVAVHLRNDADWVRVCEHIDTTTNRPLFASEQCLGEGHHLGTLTKEI
CSPSKQQILEQIVEKVGSIGAKSVFVASDKDHMIDEINEALKPYIEAHRQ
EPDDMYTSLAIMGRADLFVGNCVSTFSHIVKRERDHAGPRPSAFFGI
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 chain3zy3 Chain B Residue 1381 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3zy3 Structural Insights Into the Mechanism of Protein O-Fucosylation.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		R40 F41 G42 N43 H238 R240 A307 S308 D309 D334 M336 S355 T356 F357
Binding residue
(residue number reindexed from 1)		R15 F16 G17 N18 H208 R210 A277 S278 D279 D303 M305 S324 T325 F326
Annotation score4
Binding affinityMOAD: Kd=0.35uM
Enzymatic activity
Enzyme Commision number 2.4.1.221: peptide-O-fucosyltransferase.
Gene Ontology
Molecular Function
GO:0008417 fucosyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0046922 peptide-O-fucosyltransferase activity
Biological Process
GO:0006004 fucose metabolic process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0007219 Notch signaling pathway
GO:0036066 protein O-linked fucosylation
Cellular Component
GO:0005783 endoplasmic reticulum

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3zy3, PDBe:3zy3, PDBj:3zy3
PDBsum3zy3
PubMed21966509
UniProtQ18014|OFUT1_CAEEL GDP-fucose protein O-fucosyltransferase 1 (Gene Name=pfut-1)

[Back to BioLiP]