Structure of PDB 8cgd Chain t Binding Site BS01

Receptor Information
>8cgd Chain t (length=92) Species: 679895 (Escherichia coli BW25113) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQGIVEK
EAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI
Ligand information
>8cgd Chain a (length=2748) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gcgucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccg
aagcugcggcagcgacgcguuguuggguaggggagcguucuguaagccug
cgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcuga
cauaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaagg
guuccuguccaacguuaaucggggcagggugagucgaccccuaaggcgag
gccgaaaggcguagucgaugggaaacagguuaauauuccuguacuuggug
uuacugcgaaggggggacggagaaggcuauguuggccgggcgacgguugu
cccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaag
gcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcccug
cuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccccaaa
ccgacacagguggucagguagagaauaccaaggcgcuugagagaacucgg
gugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgcug
auauguaggugaggucccucgcggauggagcugaaaucagucgaagauac
cagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaa
guggacguauacggugugacgccugcccggugccggaagguuaauugaug
ggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaauggcguaaugauggccaggcugucuccacccgagacucag
ugaaauugaacucgcugugaagaugcaguguacccgcggcaagacggaaa
gaccccgugaaccuuuacuauagcuugacacugaacauguucuaacguug
acccguaauccggguugcggacagugucugguggguaguuugacuggggc
ggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugg
ucggacaucaggagguuagugcaauggcauaagccagcuugacugcgagc
gugacggcgcgagcaggugcgaaagcaggucauagugauccggugguucu
gaauggaagggccaucgcucaacggauaaaagguacuccggggauaacag
gcugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgau
gucggcucaucacauccuggggcugaaguaggucccaaggguauggcugu
ucgccauuuaaagugguacgcgagcuggguuuagaacgucgugagacagu
ucggucccuaucugccgugggcgcuggagaacugaggggggcugcuccua
guacgagaggaccggaguggacgcaucacugguguucggguugucaugcc
aauggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcau
cuaagcacgaaacuugccccgagaugaguucucccugacccuuuaagggu
ccugaaggaacguugaagacgacgacguugauaggccggguguguaagcg
cagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaacc
<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<<..>>>
>>>>..>>>>...<............>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.<<<<.....>>>>..>>..
.>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<..<<<<<..<<........
<..>....>>..>>>>>.>>...........))).....>>>>>>.>>>.
..>>>>>>><<<<<<<..>>>>>>>....>>>>>>..<<<<<...<<<..
....<<<<<<<<....>>>>>>>>...>>>..>>>>>........>>>>>
><......<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<
...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<...
<<<....>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<
<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((...
>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>
>>>...>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>...
>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>.....
<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<
<<<.<<...............<<<<<...............>>>>><<<<
<<.....<<<...<<<<.....>>>>...>>>...>>>>>>.........
...<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....
>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<....<...<
<<<<..<<....>>...>>>>>..>.....>>>>>>>>..>>>>><<<<<
<.......>>>>>>........<...........<<<<<<.....>>>>>
>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>
>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[...
...<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<..>>>>...<<<.<
<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....
>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<
.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<
<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.((
..>>>>..))>>>>>>>.............>>>>..]]>>>>.......<
<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>......
.<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<...
..>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>
>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<..
.............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<)))
.>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<........
...>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>
><....<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<
<<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8cgd Structural conservation of antibiotic interaction with ribosomes.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		K4 R6 R7 L14 G16 K17 V42 K43 K44 H45 Q46 G57 I58 Q66 S68 N69 R82 G84 F85 F87 K91 K92 K97
Binding residue
(residue number reindexed from 1)		K3 R5 R6 L13 G15 K16 V41 K42 K43 H44 Q45 G46 I47 Q55 S57 N58 R71 G73 F74 F76 K80 K81 K86
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0070180 large ribosomal subunit rRNA binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
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:8cgd, PDBe:8cgd, PDBj:8cgd
PDBsum8cgd
PubMed37550453
UniProtP60624|RL24_ECOLI Large ribosomal subunit protein uL24 (Gene Name=rplX)

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