Structure of PDB 8cgd Chain x Binding Site BS01

Receptor Information

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

KAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVA
RVKTLLNEKA

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): K2 A3 K4 R7 Q39 S40 H41 L43 K44 R47 R48 A51 R52 K54 T55 N58 E59
• Binding residue (residue number reindexed from 1): K1 A2 K3 R6 Q38 S39 H40 L42 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:8cgd, PDBe:8cgd, PDBj:8cgd
• PDBsum: 8cgd
• PubMed: 37550453
• UniProt: P0A7M6|RL29_ECOLI Large ribosomal subunit protein uL29 (Gene Name=rpmC)