Structure of PDB 8cgk Chain 0 Binding Site BS01

Receptor Information

>8cgk Chain 0 (length=50) Species: 679895 (Escherichia coli BW25113)

IREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKI

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): R6 K8 F20 Y21 T23 T24 K25 N26 K30 L34 L36 K37 F39 R44 H46
• Binding residue (residue number reindexed from 1): R2 K4 F16 Y17 T19 T20 K21 N22 K26 L30 L32 K33 F35 R40 H42

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

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:8cgk, PDBe:8cgk, PDBj:8cgk
• PDBsum: 8cgk
• PubMed: 37550453
• UniProt: P0A7N9|RL33_ECOLI Large ribosomal subunit protein bL33 (Gene Name=rpmG)