Structure of PDB 8i9z Chain CW Binding Site BS02

Receptor Information
>8i9z Chain CW (length=537) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SWTAFNPPLPQWILDYVSSMGYEQPTPVQKSCLDIFRGNKDVVVEAVTGS
GKTLAFLIPVVERLLRLDEAAKKHHVQAIIISPTRELASQIYNVLVSLIK
FHPESSELLQYAKSDEKRPATTKPVIVPQLLVGGTVKAAEDLSIFLRLSP
NLLVGTPGRLAELLSSPYVKTPASSFEVLVMDEADRLLDLGFSPELTRIL
GYLPKQRRTGLFSASLSDAVERLITVGMLYPHKITVRVEERKTPMSLQMS
YIVTPASHKIPALCQILEKLDPRPQRSIVFFSTCFAVKYFARVLHGILPA
GYSIVSLHGKLEPHVREKNYERFVTATSPTVLLTTDIAARGLDIPQVDLV
IQHDPPTDTKVFIHRCGRAGRAGRRGLSVVMLQPGREEGYVQLLEVRQTP
ITPLEHPQISVTDTQADDVANKIREQAKKDREVFQLAQRAFVSWARSYME
HQATSIFRVADLDWFDLAKGYGLLELPKMPETRAWSGKHEQEELRQLRKE
KKRRKKEALKMARMTEKEKEELRKLEELINEVRKRNQ
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8i9z Chain CW Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8i9z Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y35 Q37 T39 Q42 G62 S63 G64 K65 T66 D365 R393
Binding residue
(residue number reindexed from 1)		Y22 Q24 T26 Q29 G49 S50 G51 K52 T53 D343 R371
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005730 nucleolus

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8i9z, PDBe:8i9z, PDBj:8i9z
PDBsum8i9z
PubMed37129998
UniProtG0RYG4

[Back to BioLiP]