Structure of PDB 8tg5 Chain A Binding Site BS01

Receptor Information
>8tg5 Chain A (length=177) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRFKVSKLMAYILRHSPWEFGLEPDEEGFVSIEELVNAVRKVYPWVTEEY
IREIVERDEKGRYEIRGNKIRARYGHSYPVILRHEEDKESKVLYHGTVRR
NLKGIMREGIKPMKRQYVHLSINYEDAYNTGMRHGEDVVVLIIDAECLRN
KGYKILKAGKKVRIVKHVPVDCISGIL
Ligand information
Ligand ID9S2
InChIInChI=1S/C30H38N15O19P3/c31-22-13-25(37-4-34-22)43(7-40-13)28-17(48)16(47)11(60-28)2-57-67(55,56)64-20-12(61-30(21(20)62-65(50,51)52)45-9-42-15-24(33)36-6-39-27(15)45)3-58-66(53,54)63-19-10(1-46)59-29(18(19)49)44-8-41-14-23(32)35-5-38-26(14)44/h4-12,16-21,28-30,46-49H,1-3H2,(H,53,54)(H,55,56)(H2,31,34,37)(H2,32,35,38)(H2,33,36,39)(H2,50,51,52)/t10-,11-,12-,16-,17-,18+,19?,20-,21-,28+,29-,30?/m1/s1
InChIKeyQNZAOYRRZJFVRM-ZNIXMAFJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@H](O[C@H]([C@@H]4OP(=O)(O)O)n5cnc6c5ncnc6N)COP(=O)(O)O[C@@H]7[C@H](O[C@H]([C@@H]7O)n8cnc9c8ncnc9N)CO)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[CH]4[CH](CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO)n6cnc7c(N)ncnc67)O[CH]([CH]4O[P](O)(O)=O)n8cnc9c(N)ncnc89)[CH](O)[CH]3O
CACTVS 3.385Nc1ncnc2n(cnc12)[C@H]3O[C@H](CO[P](O)(=O)O[C@@H]4[C@H](CO[P](O)(=O)O[C@@H]5[C@H](O)[C@@H](O[C@@H]5CO)n6cnc7c(N)ncnc67)O[C@@H]([C@@H]4O[P](O)(O)=O)n8cnc9c(N)ncnc89)[C@@H](O)[C@H]3O
ACDLabs 12.01Nc1ncnc2c1ncn2C1OC(CO)C(OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(OP(=O)(O)O)C2OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(O)C2O)C1O
OpenEye OEToolkits 2.0.7c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(OC(C4OP(=O)(O)O)n5cnc6c5ncnc6N)COP(=O)(O)OC7C(OC(C7O)n8cnc9c8ncnc9N)CO)O)O)N
FormulaC30 H38 N15 O19 P3
Name(2S,3R,4R,5S)-2-(6-amino-9H-purin-9-yl)-4-{[(S)-{[(2R,3S,4R,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-5-({[(S)-{[(2R,3R,4S,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy}(hydroxy)phosphoryl]oxy}methyl)oxolan-3-yl dihydrogen phosphate (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain8tg5 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8tg5 Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
F3 S6 K7 A10 Y11 R14 H15 K60 R62 Y74
Binding residue
(residue number reindexed from 1)
F3 S6 K7 A10 Y11 R14 H15 K60 R62 Y74
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.1.-
Gene Ontology
Molecular Function
GO:0000215 tRNA 2'-phosphotransferase activity
GO:0016740 transferase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
Biological Process
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:8tg5, PDBe:8tg5, PDBj:8tg5
PDBsum8tg5
PubMed37883434
UniProtO57899|KPTA_PYRHO Probable RNA 2'-phosphotransferase (Gene Name=kptA)

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