Structure of PDB 8d8k Chain W Binding Site BS02

Receptor Information
>8d8k Chain W (length=395) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYKNWTNTTHTAQLQQTAVPLALPIFNFDDISKTLNKVVSYSNKQYKSLH
HLGSFKKSQFNELFQKPVCLVREDATNSFLKKLVSHPVKKFIITGEPGVG
KTVLLSQAHAYAVDSKQIIINISYPELFLNGRNDFSYDDDLKLFIQPMYL
KKLIRKILKANDPALLKSIELSKDYKFSNANPKNASVKPFVTLNKTKNTV
LDLLSVMTHPHNRGKLMKAIIDELSVQSKVPIMFTVDNFSKVLTTAYSAY
RNTENKQIYSLDLQMGKLMMDIISGETKFANGESSTILAISGVDRTNKTL
PVALGKIPVDPYVTRYHYEPKFVELLQKGNVTEFEVPKLNKQEVNELIDY
YKQSNVLLDKDITGKKWENLIDEKYFLSGNGNPRELLKSLVLSHR
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[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
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain8d8k Chain W 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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PDB8d8k Principles of mitoribosomal small subunit assembly in eukaryotes.
Resolution3.13 Å
Binding residue
(original residue number in PDB)		Q114 L125 G153 G155 K156 T157 V158 S346 G347 P438 R439
Binding residue
(residue number reindexed from 1)		Q59 L70 G98 G100 K101 T102 V103 S291 G292 P383 R384
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0005524 ATP binding
GO:0005525 GTP binding
Biological Process
GO:0032543 mitochondrial translation
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005763 mitochondrial small ribosomal subunit
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8d8k, PDBe:8d8k, PDBj:8d8k
PDBsum8d8k
PubMed36482135
UniProtQ01163|RT23_YEAST Small ribosomal subunit protein mS29 (Gene Name=RSM23)

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