Structure of PDB 8cgd Chain n Binding Site BS01

Receptor Information

>8cgd Chain n (length=116) Species: 679895 (Escherichia coli BW25113)

DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAA
STVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHG
RVQALADAAREAGLQF

Ligand information

>8cgd Chain a (length=2748)

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

Structure summary

• PDB: 8cgd Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): R9 R10 T12 R13 R16 K17 L18 L21 S91 F92 R94 Q98 Y99 R111 F117
• Binding residue (residue number reindexed from 1): R8 R9 T11 R12 R15 K16 L17 L20 S90 F91 R93 Q97 Y98 R110 F116

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• 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

External links

• PDB: RCSB:8cgd, PDBe:8cgd, PDBj:8cgd
• PDBsum: 8cgd
• PubMed: 37550453
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)