Structure of PDB 8cgk Chain v Binding Site BS01

Receptor Information

>8cgk Chain v (length=75) Species: 679895 (Escherichia coli BW25113)

RNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLF
AKADGKVKFEVKGPKNRKFISIEAE

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): N12 R14 D15 S16 E17 A18 K19 R20 K24 F26 G27 E29 A33 G34 S35 I36 R41 G42 T43 H46 G54 R55 D56 H57 T58 F60 F69 K75 R77 K78
• Binding residue (residue number reindexed from 1): N2 R4 D5 S6 E7 A8 K9 R10 K14 F16 G17 E19 A23 G24 S25 I26 R31 G32 T33 H36 G44 R45 D46 H47 T48 F50 F59 K65 R67 K68

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0043022 ribosome binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0001558 regulation of cell growth
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042256 cytosolic ribosome assembly
• GO:0090070 positive regulation of ribosome biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

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: P0A7L8|RL27_ECOLI Large ribosomal subunit protein bL27 (Gene Name=rpmA)