Structure of PDB 8odp Chain G Binding Site BS03

Receptor Information
>8odp Chain G (length=504) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELR
NACRGGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAA
FDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDHI
PVGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQ
ADPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHK
GQVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASP
EGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDV
SHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLI
GGTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDK
LADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGISKKAIKLRPIA
VIKG
Ligand information
Ligand IDG2P
InChIInChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-30(20,21)3-31(22,23)29-32(24,25)26/h2,4,6-7,10,17-18H,1,3H2,(H,20,21)(H,22,23)(H2,24,25,26)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
InChIKeyGXTIEXDFEKYVGY-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)C[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(C[P@@](=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O13 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
ChEMBLCHEMBL1232908
DrugBankDB03532
ZINCZINC000016051609
PDB chain8odp Chain G Residue 603 [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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PDB8odp Structure of human rtcb archease complex
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D119 C122 N226 H227 Y228 E230 H259 H353 N354 G402 G403 T404 M405 H428 A430 G431 Y475 K504
Binding residue
(residue number reindexed from 1)		D118 C121 N225 H226 Y227 E229 H258 H352 N353 G401 G402 T403 M404 H427 A429 G430 Y474 K503
Annotation score3
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
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Cellular Component
External links
PDB RCSB:8odp, PDBe:8odp, PDBj:8odp
PDBsum8odp
PubMed38493148
UniProtQ9Y3I0|RTCB_HUMAN RNA-splicing ligase RtcB homolog (Gene Name=RTCB)

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