Structure of PDB 7v08 Chain m Binding Site BS02

Receptor Information
>7v08 Chain m (length=466) Species: 1247190 (Saccharomyces cerevisiae BY4741) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GTGKKEKSRRIREGNLRVKGENFYRDSKRVKFLNMYTSGKEIRNKKGNLI
RAASFQDSTIPDARVQPDRRWFGNTRVISQDALQHFRSALGETQKDTYQV
LLRRNKLPMSLLEEKDADESPKARILDTESYADAFGPKAQRKRPRLAASN
LEDLVKATNEDITKYEEKQVLDATLGLMGNQEDKENGWTSAAKEAIFSKG
QSKRIWNELYKVIDSSDVVIHVLDARDPLGTRCKSVEEYMKKETPHKHLI
YVLNKCDLVPTWVAAAWVKHLSKERPTLAFHASITNSFGKGSLIQLLRQF
SQLHTDRKQISVGFIGYPNTGKSSIINTLRKKKVCQVAPIPGETKVWQYI
TLMKRIFLIDCPGIVPPSSKDSEEDILFRGVVRVEHVTHPEQYIPGVLKR
CQVKHLERTYEISGWKDATEFIEILARKQGRLLKGGEPDESGVSKQILND
FNRGKIPWFVLPPEKE
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 chain7v08 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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PDB7v08 rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		N260 K261 D263 H287 A288 N325 G327 K328 S329 S330 V343 A344
Binding residue
(residue number reindexed from 1)		N254 K255 D257 H281 A282 N319 G321 K322 S323 S324 V337 A338
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:7v08, PDBe:7v08, PDBj:7v08
PDBsum7v08
PubMed36864048
UniProtP53742|NOG2_YEAST Nucleolar GTP-binding protein 2 (Gene Name=NOG2)

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