Structure of PDB 8qbm Chain F Binding Site BS04

Receptor Information
>8qbm Chain F (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 H 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)
F128 R132 S133 I135 N136
Binding residue
(residue number reindexed from 1)
F126 R130 S131 I133 N134
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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