Structure of PDB 8odo Chain C Binding Site BS01

Receptor Information
>8odo Chain C (length=503) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRN
ACRGGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAAF
DMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDHIP
VGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQA
DPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKG
QVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASPE
GQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDVS
HNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLIG
GTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDKL
ADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGISKKAIKLRPIAV
IKG
Ligand information
Ligand ID5GP
InChIInChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyRQFCJASXJCIDSX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O8 P
NameGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL283807
DrugBankDB01972
ZINCZINC000002159505
PDB chain8odo Chain C Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8odo Structure of human RTCB in complex with Archease
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N226 Y228 E230 H259 G402 G403 T404 M405 H428 A430 G431 Y475 K504
Binding residue
(residue number reindexed from 1)		N224 Y226 E228 H257 G400 G401 T402 M403 H426 A428 G429 Y473 K502
Annotation score4
Enzymatic activity
Enzyme Commision number 6.5.1.8: 3'-phosphate/5'-hydroxy nucleic acid ligase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003972 RNA ligase (ATP) activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008452 RNA ligase activity
GO:0016874 ligase activity
GO:0016886 ligase activity, forming phosphoric ester bonds
GO:0017166 vinculin binding
GO:0046872 metal ion binding
GO:0170057 RNA ligase (GTP) activity
Biological Process
GO:0001701 in utero embryonic development
GO:0001890 placenta development
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
GO:0006396 RNA processing
GO:0008033 tRNA processing
Cellular Component
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle
GO:0072669 tRNA-splicing ligase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8odo, PDBe:8odo, PDBj:8odo
PDBsum8odo
PubMed38493148
UniProtQ9Y3I0|RTCB_HUMAN RNA-splicing ligase RtcB homolog (Gene Name=RTCB)

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