Structure of PDB 8cgk Chain x Binding Site BS01

Receptor Information

>8cgk Chain x (length=60) Species: 679895 (Escherichia coli BW25113)

KAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVA
RVKTLLNEKA

Ligand information

>8cgk Chain a (length=2699)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaaaacccgaugcaaacugcgaaua
ccggagaauguuaucacgggagacacacggcgggugcuaacguccgucgu
gaagagggaaacaacccagaccgccagcuaaggucccaaagucaugguua
agugggaaacgaugugggaaggcccagacagcgucgagucggccugcgcg
gaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgacgcgu
uguuggguaggggagcguucuguaagccugcgaaggugugcugugaggca
ugcuggagguaucagaagugcgaaugcugacauaaguaacgauaaagcgg
gugaaaagcccgcucgccggaagaccaaggguuccuguccaacguuaauc
ggggcagggugagucgaccccuaaggcgaggccgaaaggcguagucgaug
ggaaacagguuaauauuccuguacuugguguuacugcgaaggggggacgg
agaaggcuauguuggccgggcgacgguugucccgguuuaagcguguaggc
ugguuuuccaggcaaauccggaaaaucaaggcugaggcgugaugacgagg
cacuacggugcugaagcaacaaaugcccugcuuccaggaaaagccucuaa
gcaucagguaacaucaaaucguaccccaaaccgacacagguggucaggua
gagaauaccaaggcgcuugagagaacucgggugaaggaacuaggcaaaau
ggugccguaacuucgggagaaggcacgcugauauguaggugaggucccuc
gcggauggagcugaaaucagucgaagauaccagcuggcugcaacuguuua
uuaaaaacacagcacugugcaaacacgaaaguggacguauacggugugac
gccugcccggugccggaagguuaauugaugggguuagcgcaagcgaagcu
cuugaucgaagccccgguaaacggcggccuaagguagcgaaauuccuugu
cggguaaguuccgaccugcacgaauggcguaaugauggccaggcugucuc
cacccgagacucagugaaauugaacucgcugugaagaugcaguguacccg
cggcaagacggaaagaccccgugaaccuuuacuauagcuugacacugaac
auguucuaacguugacccguaauccggguugcggacagugucuggugggu
aguuugacuggggcggucuccuccuaaagaguaacggaggagcacgaagg
uuggcuaauccggagguuagugcaauggcauaagccagcuugacugcgag
cgugacggcgcgagcaggugcgaaagcaggucauagugauccggugguuc
ugaauggaagggccaucgcucaacggauaaaagguacuccggggauaaca
ggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccucga
ugucggcucaucacauccuggggcugaaguaggucccaaggguauggcug
uucgccauuuaaagugguacgcgagcuggguuuagaacgucgugagacag
uucggucccuaucugccgugggcgcuggagaacugaggggggcugcuccu
aguacgagaggaccggaguggacgcaucacugguguucggguugucaugc
caauggcacugcccgguagcuaaaugcggaagagauaagugcugaaagca
ucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaaggg
uccugaaggaacguugaagacgacgacguugauaggccggguguguaagc
gcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaacc

<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<<..>>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<.<....<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>..>>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<<..>>>
>>>>..>>>>...<............>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<......>>>>.>>>..>>.>.....
>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<......>>>>>>>>>
>....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<..
.........<<..<<<<<..<<................>>..>>>>>.>>
...........))).....>>>>>>.>>>...>>>>>>><<<<<......
>>>>>....>>>>>>..<<<<<...<<<......<<<<<<<<....>>>>
>>>>...>>>..>>>>>........>>>>>><......<<.....<<<<<
<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<.<<<...<<<...<<<....>>>...>>>...>
>>..<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....<<
<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<<...<<<
<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>>...>><..<<
<<<....>>>>>...>>>>>>...>>>...>>>>.........>>>>...
>>....>>>>>>>>>>>.>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>>..<<<<....<<<<<<<<.<<..............
.<<<<<...............>>>>><<<<<<.....<<<...<<<<...
..>>>>...>>>...>>>>>>............<<<<<<<<<..<<<...
......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<
<<<.<<<..<<<<<<<..<<<<...<...<<<<<..<<....>>...>>>
>>.>.....>>>>>>>>>..>>>>>...........<...........<<
<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.
>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<
<<<<.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<.
...>>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>
>>>..<<<<.....>>>><<<<<<...........>>>>>>.(<<...<<
<<<<<...<<..>>.....<<)..(((>>....>>>>>>>...<<<<..<
<<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.(
(..>>>>..))>>>>>>>.............>>>>..]]>>>>.......
<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>.....
..<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<..
...>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>
>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.
..............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))
).>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<.......
....>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>
>><....<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<
<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cgk Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 1.64 Å
• Binding residue (original residue number in PDB): A3 K4 R7 Q39 S40 H41 K44 R47 R48 A51 R52 K54 T55 N58 E59
• Binding residue (residue number reindexed from 1): A2 K3 R6 Q38 S39 H40 K43 R46 R47 A50 R51 K53 T54 N57 E58

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cgk, PDBe:8cgk, PDBj:8cgk
• PDBsum: 8cgk
• PubMed: 37550453
• UniProt: P0A7M6|RL29_ECOLI Large ribosomal subunit protein uL29 (Gene Name=rpmC)