Structure of PDB 8dcd Chain A Binding Site BS03

Receptor Information
>8dcd Chain A (length=481) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNV
AMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGV
RLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVD
GAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGS
GNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLR
IMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMIT
HWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHR
KGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFG
STCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGA
YKNVDNVVKVVSEAGIAKLVARMRPIGVAKG
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 chain8dcd Chain A Residue 501 [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]
PDB8dcd Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Resolution2.22 Å
Binding residue
(original residue number in PDB)		D95 C98 G201 N202 H203 F204 E206 H234 P378 G379 S380 M381 H404 A406 G407 Y451 K480
Binding residue
(residue number reindexed from 1)		D95 C98 G201 N202 H203 F204 E206 H234 P378 G379 S380 M381 H404 A406 G407 Y451 K480
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
View graph for
Biological Process
External links
PDB RCSB:8dcd, PDBe:8dcd, PDBj:8dcd
PDBsum8dcd
PubMed36130078
UniProtO59245|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)

[Back to BioLiP]