Structure of PDB 8dcf Chain A Binding Site BS02

Receptor Information
>8dcf Chain A (length=480) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVA
MLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVR
LIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDG
AKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSG
NHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRI
MERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITH
WVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRK
GATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGS
TCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAY
KNVDNVVKVVSEAGIAKLVARMRPIGVAKG
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[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=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8dcf Chain A Residue 601 [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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PDB8dcf Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Resolution2.42 Å
Binding residue
(original residue number in PDB)		D95 C98 N202 F204 E206 H234 P378 G379 S380 M381 A406 G407 Y451 K480
Binding residue
(residue number reindexed from 1)		D94 C97 N201 F203 E205 H233 P377 G378 S379 M380 A405 G406 Y450 K479
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.-.-
6.5.1.8: 3'-phosphate/5'-hydroxy nucleic acid ligase.
Gene Ontology
Molecular Function
GO:0008452 RNA ligase activity
Biological Process
GO:0006396 RNA processing

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:8dcf, PDBe:8dcf, PDBj:8dcf
PDBsum8dcf
PubMed36130078
UniProtO59245|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)

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