Structure of PDB 8qrl Chain X Binding Site BS03

Receptor Information
>8qrl Chain X (length=352) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AISRTNENDPAKHGDQHEGQHYNISPQDLETVFPHGLPPRFVMQVKTFSE
ACLMVRKPALELLHYLKNTSFAYPAIRYLLYGEKGTGKTLSLCHVIHFCA
KQDWLILHIPDAHLWVKNCRDLLQSSYNKQRFDQPLEASTWLKNFKTTNE
RFLNQIKVQEKYVWNKRESTEKGSPLGEVVEQGITRVRNATDAVGIVLKE
LKRQSSLGMFHLLVAVDGINALWGRTTLKREDKSPIAPEELALVHNLRKM
MKNDWHGGAIVSALSQTGSLFKPRKAYLPQELLGKEGFDALDPFIPILVS
NYNPKEFESCIQYYLENNWLQHEKAPTEEGKKELLFLSNANPSLLERHCA
YL
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 chain8qrl Chain X Residue 503 [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]
PDB8qrl GTPBP8 plays a role in mitoribosome formation in human mitochondria.
Resolution3.34 Å
Binding residue
(original residue number in PDB)		Y173 R177 Y208 V209 D238 G241 I242 K295
Binding residue
(residue number reindexed from 1)		Y127 R131 Y162 V163 D192 G195 I196 K249
Annotation score4
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0006915 apoptotic process
GO:0032543 mitochondrial translation
GO:0097190 apoptotic signaling pathway
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005763 mitochondrial small ribosomal subunit
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8qrl, PDBe:8qrl, PDBj:8qrl
PDBsum8qrl
PubMed38969660
UniProtP51398|RT29_HUMAN Small ribosomal subunit protein mS29 (Gene Name=DAP3)

[Back to BioLiP]