Structure of PDB 8cgd Chain f Binding Site BS01

Receptor Information

>8cgd Chain f (length=154) Species: 679895 (Escherichia coli BW25113)

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVSAKSFDGRGNYSMGVREQIILDITITTTAKSDEEGRALLAAFD
FPFR

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): K33 T35 N37 M38 G39 G41 T68 R71 K72 F77 I79 I85 K88 S121 F122 D123 N127 S129 G131 L152 D153 T155 T157
• Binding residue (residue number reindexed from 1): K32 T34 N36 M37 G38 G40 T67 R70 K71 F76 I78 I84 K87 S111 F112 D113 N117 S119 G121 L128 D129 T131 T133

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• 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:0005829 cytosol
• 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: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)