Structure of PDB 8qbm Chain H Binding Site BS02

Receptor Information
>8qbm Chain H (length=302) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKFTDEQQQQLIGHLTKKGFYRGANIKITIFLCGGDVANHQSWRHQLSQF
LAKFSDVDIFYPEDLFDDLLAGQGQHSLLSLENILAEAVDVIILFPESPG
SFTELGAFSNNENLRRKLICIQDAKFKSKRSFINYGPVRLLRKFNSKSVL
RCSSNELKEMCDSSIDVARKLRLYKKLMASIKKVRKENKVSKDIGNILYA
ERFLLPCIYLLDSVNYRTLCELAFKAIKQDDVLSKIIVRSVVSRLINERK
ILQMTDGYQVTALGASYVRSVFDRKTLDRLRLEIMNFENRRKSTFNYDKI
PY
Ligand information
Ligand IDAR6
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
InChIKeySRNWOUGRCWSEMX-ZQSHOCFMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N
ACDLabs 12.01O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC15 H23 N5 O14 P2
Name[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE;
Adenosine-5-Diphosphoribose
ChEMBL
DrugBankDB02059
ZINCZINC000014880207
PDB chain8qbm Chain F Residue 401 [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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PDB8qbm Retron-Eco1 assembles NAD + -hydrolyzing filaments that provide immunity against bacteriophages.
Resolution3.09 Å
Binding residue
(original residue number in PDB)
Q124 F128 S133 F134
Binding residue
(residue number reindexed from 1)
Q122 F126 S131 F132
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0051607 defense response to virus

View graph for
Biological Process
External links
PDB RCSB:8qbm, PDBe:8qbm, PDBj:8qbm
PDBsum8qbm
PubMed38788717
UniProtP0DV88|RIB86_ECOLX Retron Ec86 putative ribosyltransferase/DNA-binding protein (Gene Name=LM2_00875)

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