Structure of PDB 8cgk Chain e Binding Site BS01

Receptor Information

>8cgk Chain e (length=201) Species: 679895 (Escherichia coli BW25113)

MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRA
EVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKM
YRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIIT
GELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEML
A

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): N24 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 V52 T53 G54 S55 G56 K57 K58 Q62 K63 G64 G66 R67 A68 R69 G71 S75 P76 I77 W78 R79 S80 V83 T84 F85 P89 Q90 Q94 K95 N97 K98 K99 M100 Y101 R102 P129 K130 T131 L159 R162 N163 L164 H165 T173
• Binding residue (residue number reindexed from 1): N24 H29 Q30 Y35 A36 A39 R40 Q41 T43 R44 A45 Q46 K47 T48 R49 A50 V52 T53 G54 S55 G56 K57 K58 Q62 K63 G64 G66 R67 A68 R69 G71 S75 P76 I77 W78 R79 S80 V83 T84 F85 P89 Q90 Q94 K95 N97 K98 K99 M100 Y101 R102 P129 K130 T131 L159 R162 N163 L164 H165 T173

Gene Ontology

Molecular Function

• GO:0001070 RNA-binding transcription regulator activity
• GO:0003677 DNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0030371 translation repressor activity
• GO:0048027 mRNA 5'-UTR binding
• GO:0060698 endoribonuclease inhibitor activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006353 DNA-templated transcription termination
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0031555 transcriptional attenuation
• GO:0042255 ribosome assembly
• GO:0045892 negative regulation of DNA-templated transcription
• GO:0046677 response to antibiotic
• GO:2000766 negative regulation of cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8cgk, PDBe:8cgk, PDBj:8cgk
• PDBsum: 8cgk
• PubMed: 37550453
• UniProt: P60723|RL4_ECOLI Large ribosomal subunit protein uL4 (Gene Name=rplD)