Structure of PDB 8c9b Chain E Binding Site BS01

Receptor Information
>8c9b Chain E (length=148) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGASQKVNKKMYRG
ALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGEL
DENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA
Ligand information
>8c9b Chain A (length=574) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gcguacacgguggaugcccuggcagucagaggcgaugaaggacgugcuaa
ucugcgauaagcgucgguaaggugauaugaaccguuauaaccggcgauuu
ccgaauggggaaacccaguguguuucgacacacuaucauuaacugaaucc
auagguuaaugaggcgaaccgggggaacugaaacaucuaaguaccccgag
gaaaagaaaucaaccgagauucccccaguagcggcgagcgaacggggagc
agcccagagccugaaucaguguguguguuaguggaagcgucuggaaaggc
gcgcgauacagggugacagccccguacacaaaaaugcacaugcugugagc
ucgaugaguagggcgggacacgugguauccugucugaauauggggggacc
auccuccaaggcuaaauacuccugacugaccgauagugaaccaguaccgu
gagggaaaggcgaaaagaaccccggcgaggggagugaaaaagaaccugaa
accguguacguuuauauucuguagcaagguuaaccgaauaggggagccga
agggaaaccgaaguugcaggguau
.<<<<<<<<<<....<.<<.<<<<<<<<<<<<<......<<<<<<.[..(
((.>>>.....<<<<<<<..<<<)))..].>>>......>>>>>>>...>
>>....<<<....>>><<<<<<<....>>>>>>>.<<<<<<<<<......
...>>>>>>>>>.>>...<<<<<<...................>>>>>.>
.........<<....>>..<<<<.<<....<<.....>>....>>>>>>.
.<<<..<<<<......<<<<<<<<<<<<<.<<<...<<<<<......>>>
>>((......<<<.....))>>>...>>>...>>>>>>>>>>>>>...>>
>>........<<<.<<<..........>.>>.>>>......<<<<<....
.>>>>>...>>>......>>.>>>>>>>.>>...............<<..
..>>....>>.........<<<<.....>>>>.............>....
>>>>>>>>>>...<<<<<<<<<<<<..<<....<<.....>>....>>..
.<<....>>...>>>>>>>>>>>>
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]
PDB8c9b Cryo-EM captures early ribosome assembly in action.
Resolution5.9 Å
Binding residue
(original residue number in PDB)		N24 L27 Q30 Y35 Q94 K95 V96 N97 K98 K99 M100 K130 T131 K132 L159 R162 N163 T173
Binding residue
(residue number reindexed from 1)		N24 L27 Q30 Y35 Q41 K42 V43 N44 K45 K46 M47 K77 T78 K79 L106 R109 N110 T120
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001070 RNA-binding transcription regulator activity
GO:0003677 DNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0030371 translation repressor activity
GO:0048027 mRNA 5'-UTR binding
GO:0060698 endoribonuclease inhibitor activity
Biological Process
GO:0002181 cytoplasmic translation
GO:0006353 DNA-templated transcription termination
GO:0006412 translation
GO:0006417 regulation of translation
GO:0017148 negative regulation of translation
GO:0031555 transcriptional attenuation
GO:0042255 ribosome assembly
GO:0045892 negative regulation of DNA-templated transcription
GO:0046677 response to antibiotic
GO:2000766 negative regulation of cytoplasmic translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8c9b, PDBe:8c9b, PDBj:8c9b
PDBsum8c9b
PubMed36797249
UniProtP60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)

[Back to BioLiP]