Structure of PDB 6ylh Chain m Binding Site BS02

Receptor Information
>6ylh Chain m (length=439) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGKKEKSRRIREGRVKGENFYRDSKRVKFLNMYTSGKEIRNKKGNLIRAA
SFQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQKDTYQVLLR
RNKLPMSLLARILDTESYADAFGPKAQRKRPRLAASNLEDLVKATNEDIT
KYEEKQVLDAENGWTSAAKEAIFSKGQSKRIWNELYKVIDSSDVVIHVLD
ARDPLGTRCKSVEEYMKKETPHKHLIYVLNKCDLVPTWVAAAWVKHLSKE
RPTLAFHASITNSFGKGSLIQLLRQFSQLHTDRKQISVGFIGYPNTGKSS
IINTLRKKKVCQVAPIPGETKVWQYITLMKRIFLIDCPGIVPPSSKDSEE
DILFRGVVRVEHVTHPEQYIPGVLKRCQVKHLERTYEISGWKDATEFIEI
LARKQGRLLKGGEPDESGVSKQILNDFNRGKIPWFVLPP
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 chain6ylh Chain m Residue 501 [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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PDB6ylh Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		N260 K261 D263 H287 A288 N325 G327 K328 S329 S330 V343 A344 P345 T350
Binding residue
(residue number reindexed from 1)		N230 K231 D233 H257 A258 N295 G297 K298 S299 S300 V313 A314 P315 T320
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0070180 large ribosomal subunit rRNA binding
Biological Process
GO:0000055 ribosomal large subunit export from nucleus
GO:0042254 ribosome biogenesis
GO:2000200 regulation of ribosomal subunit export from nucleus
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0030687 preribosome, large subunit precursor

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ylh, PDBe:6ylh, PDBj:6ylh
PDBsum6ylh
PubMed32668200
UniProtP53742|NOG2_YEAST Nucleolar GTP-binding protein 2 (Gene Name=NOG2)

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