Structure of PDB 6x5t Chain F Binding Site BS01

Receptor Information
>6x5t Chain F (length=467) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGKDHEILRRRIENGAKELWFFLQSELKKLKNLEGNELQRHADEFLLDLG
HHERSIMTDLYYLSQTDGAGDWREKEAKDLTELVQRRITYLQNPKDCSKA
KKLVCNINKGCGYGCQLHHVVYCFMIAYGTQRTLILESQNWRYATGGWET
VFRPVSETCTDRSGISTGHWSGEVKDKNVQVVELPIVDSLHPRPPYLPLA
VPEDLADRLVRVHGDPAVWWVSQFVKYLIRPQPWLEKEIEEATKKLGFKH
PVIGVHVRRTDKVGTEAAFHPIEEYMVHVEEHFQLLARRMQVDKKRVYLA
TDDPSLLKEAKTKYPNYEFISDNSISWSAGLHNRYTENSLRGVILDIHFL
SQADFLVCTFSSQVCRVAYEIMQTLHPDASANFHSLDDIYYFGGQNAHNQ
IAIYAHQPRTADEIPMEPGDIIGVAGNHWDGYSKGVNRKLGRTGLYPSYK
VREKIETVKYPTYPEAE
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 chain6x5t Chain F Residue 600 [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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PDB6x5t Characterizing human alpha-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases.
Resolution2.47 Å
Binding residue
(original residue number in PDB)		G219 Y220 G221 C222 Y250 H363 R365 K369 A407 T408 A436 R441 V450 D453 S469 Q470 V471
Binding residue
(residue number reindexed from 1)		G112 Y113 G114 C115 Y143 H256 R258 K262 A300 T301 A329 R334 V343 D346 S362 Q363 V364
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.68: glycoprotein 6-alpha-L-fucosyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008424 glycoprotein 6-alpha-L-fucosyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0017124 SH3 domain binding
GO:0046921 alpha-(1->6)-fucosyltransferase activity
Biological Process
GO:0001701 in utero embryonic development
GO:0006486 protein glycosylation
GO:0006487 protein N-linked glycosylation
GO:0006491 N-glycan processing
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0007229 integrin-mediated signaling pathway
GO:0007585 respiratory gaseous exchange by respiratory system
GO:0009312 oligosaccharide biosynthetic process
GO:0010468 regulation of gene expression
GO:0010761 fibroblast migration
GO:0016477 cell migration
GO:0018279 protein N-linked glycosylation via asparagine
GO:0019082 viral protein processing
GO:0036071 N-glycan fucosylation
GO:0042355 L-fucose catabolic process
GO:0043112 receptor metabolic process
GO:0046368 GDP-L-fucose metabolic process
GO:1900407 regulation of cellular response to oxidative stress
Cellular Component
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0032580 Golgi cisterna membrane
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6x5t, PDBe:6x5t, PDBj:6x5t
PDBsum6x5t
PubMed33004438
UniProtQ9BYC5|FUT8_HUMAN Alpha-(1,6)-fucosyltransferase (Gene Name=FUT8)

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