Structure of PDB 8cgd Chain i Binding Site BS01

Receptor Information
>8cgd Chain i (length=141) Species: 679895 (Escherichia coli BW25113) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTG
DYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVI
EIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI
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)		K2 T3 T5 K7 E9 W15 T24 G26 R27 T30 R37 K39 H47 Y53 T65 K68 K72 Y75 H76 H77 T78 H80 I81 G82 I84 R95 R96 E102 A104 G107 M108 P113 L114 R116 R120 K123 N131 H132 A134 Q135 Q136
Binding residue
(residue number reindexed from 1)		K1 T2 T4 K6 E8 W14 T23 G25 R26 T29 R36 K38 H46 Y52 T64 K67 K71 Y74 H75 H76 T77 H79 I80 G81 I83 R94 R95 E101 A103 G106 M107 P112 L113 R115 R119 K122 N130 H131 A133 Q134 Q135
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
GO:0008270 zinc ion binding
GO:0048027 mRNA 5'-UTR binding
GO:0070180 large ribosomal subunit rRNA binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0017148 negative regulation of 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
UniProtP0AA10|RL13_ECOLI Large ribosomal subunit protein uL13 (Gene Name=rplM)

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