Structure of PDB 7ug6 Chain m Binding Site BS02

Receptor Information
>7ug6 Chain m (length=469) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GTGKKEKSRRIREGDTKDGNLRVKGENFYRDSKRVKFLNMYTSGKEIRNK
KGNLIRAASFQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQK
DTYQVLLRRNKLPMSLLEEKDADESPKARILDTESYADAFGPKAQRKRPR
LAASNLEDLVKATNEDITKYEEKQVLDATLGGNQEDKENGWTSAAKEAIF
SKGQSKRIWNELYKVIDSSDVVIHVLDARDPLGTRCKSVEEYMKKETPHK
HLIYVLNKCDLVPTWVAAAWVKHLSKERPTLAFHASITNSFGKGSLIQLL
RQFSQLHTDRKQISVGFIGYPNTGKSSIINTLRKKKVCQVAPIPGETKVW
QYITLMKRIFLIDCPGIVPPSSKDSEEDILFRGVVRVEHVTHPEQYIPGV
LKRCQVKHLERTYEISGWKDATEFIEILARKQGRLLKGGEPDESGVSKQI
LNDFNRGKIPWFVLPPEKE
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 chain7ug6 Chain m Residue 601 [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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PDB7ug6 A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		N260 K261 D263 L264 H287 P324 T326 G327 K328 S329 S330 V343 A344 P345
Binding residue
(residue number reindexed from 1)		N257 K258 D260 L261 H284 P321 T323 G324 K325 S326 S327 V340 A341 P342
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:7ug6, PDBe:7ug6, PDBj:7ug6
PDBsum7ug6
PubMed36536102
UniProtP53742|NOG2_YEAST Nucleolar GTP-binding protein 2 (Gene Name=NOG2)

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