Structure of PDB 3zy5 Chain A Binding Site BS01

Receptor Information
>3zy5 Chain A (length=356) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEATDPNGYIVFCPCMGRFGNQVDQFLGVLAFAKALDRTLVLPNFIEFKH
PETKMIPFEFLFQVGTVAKYTRVVTMQEFTKKIMPTVWPPEKRKAFCWTP
RQAIYAEPGCHSKEGNPFGPYWDQIDVSFVGDEYFGDIPGGFDLNQMGSR
KKWLEKFPSEEYPVLAFSSAPAPFPSKGKVWSIQKYLRWSSRITEQAKKF
ISANLAKPFVAVHLRNDADWVRVCEHIDTTTNRPLFASEQCLGEGHHLGT
LTKEICSPSKQQILEQIVEKVGSIGAKSVFVASDKDHMIDEINEALKPYE
IEAHRQEPDDMYTSLAIMGRADLFVGNCVSTFSHIVKRERDHAGQSPRPS
AFFGIR
Ligand information
Ligand IDGFB
InChIInChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5+,7+,8+,9+,10+,11-,14+,15+/m0/s1
InChIKeyLQEBEXMHBLQMDB-JGQUBWHWSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)C)O)O)N
OpenEye OEToolkits 1.9.2CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O
OpenEye OEToolkits 1.9.2C[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O
CACTVS 3.385C[C@@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@H](O)[C@@H]1O
CACTVS 3.385C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)[CH](O)[CH]1O
FormulaC16 H25 N5 O15 P2
NameGUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
ChEMBLCHEMBL1229250
DrugBankDB18689
ZINCZINC000008551145
PDB chain3zy5 Chain A Residue 1386 [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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PDB3zy5 Structural Insights Into the Mechanism of Protein O-Fucosylation.
Resolution1.96 Å
Binding residue
(original residue number in PDB)		R40 G42 N43 H238 R240 W245 F261 A307 S308 D309 M336 S355 T356 F357
Binding residue
(residue number reindexed from 1)		R18 G20 N21 H213 R215 W220 F236 A282 S283 D284 M311 S330 T331 F332
Annotation score4
Binding affinityMOAD: Kd=0.23uM
PDBbind-CN: -logKd/Ki=6.64,Kd=0.23uM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3zy5, PDBe:3zy5, PDBj:3zy5
PDBsum3zy5
PubMed21966509
UniProtQ18014|OFUT1_CAEEL GDP-fucose protein O-fucosyltransferase 1 (Gene Name=pfut-1)

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