Structure of PDB 6ylg Chain b Binding Site BS03

Receptor Information
>6ylg Chain b (length=613) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKVK
YTGEGFVEKFEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISRA
KLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKKLRDPLAYLEQ
VRQHIGRLPSIDPNTRTLLICGYPNVGKSSFLRCITKSDVDVQPYAFTTK
SLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSIYAIAHLRSCVLY
FMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINTDEERAQLLESVKE
VPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKIHVAQPQARDDVKR
TPFIPESVKNLKKYDPEDPNRRKLARDIEAENGGAGVFNVNLKDKYLLED
DEWKNDIMPEILDGKNVYDFLDPEIAAKLQALEEEEEKLENEGFYNIYDG
FEASEVDDIKEKAAWIRNRQKTMIAEARNRKSLKNKAIMPRSKLTKSFGK
MEEHMSTLGHDMSALQDKQNRAARKNRYVERGSDVVFGDQDALTASTENG
VKLRQTDRLLDGVADGSMRSKADRMAKMERRERNRHAKQGESDRHNAVSL
SKHLFSVGKTDFR
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain6ylg Chain b Residue 701 [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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PDB6ylg Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		N177 V178 G179 K180 S181 V194 T201 D220 N288 C322
Binding residue
(residue number reindexed from 1)		N175 V176 G177 K178 S179 V192 T199 D218 N286 C311
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0000054 ribosomal subunit export from nucleus
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis
GO:0042273 ribosomal large subunit biogenesis
GO:1902626 assembly of large subunit precursor of preribosome
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0030687 preribosome, large subunit precursor

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ylg, PDBe:6ylg, PDBj:6ylg
PDBsum6ylg
PubMed32668200
UniProtQ02892|NOG1_YEAST Nucleolar GTP-binding protein 1 (Gene Name=NOG1)

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