Structure of PDB 8syl Chain U Binding Site BS01

Receptor Information

>8syl Chain U (length=110) Species: 562 (Escherichia coli)

METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKV
LESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRT
SHITVVVSDR

Ligand information

>8syl Chain A (length=2845)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gcgucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccg
aagcugcggcagcgacgcgcguuguuggguaggggagcguucuguaagcc
ugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcu
gacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaa
ggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggcg
aggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuugg
uguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgguu
gucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauca
aggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugccc
ugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccca
aaccgacacagguggucagguagagaauaccaaggcgcuugagagaacuc
gggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgc
ugauauguaggugaggucccucgcggauggagcugaaaucagucgaagau
accagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacga
aaguggacguauacggugugacgccugcccggugccggaagguuaauuga
ugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaauggcguaaugauggccaggcugucuccacccgagacuc
agugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgga
aagaccccgugaaccuuuacuauagcuugacacugaacauugagccuuga
uguguaggauaggugggaggcuuugaaguguggacgccagucugcaugga
gccgaccuugaaauaccacccuuuaauguuugauguucuaacguugaccc
guaauccggguugcggacagugucugguggguaguuugacuggggcgguc
uccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucgg
acaucaggagguuagugcaauggcauaagccagcuugacugcgagcguga
cggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaau
ggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcug
auaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugucg
gcucaucacauccuggggcugaaguaggucccaaggguauggcuguucgc
cauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucgg
ucccuaucugccgugggcgcuggagaacugaggggggcugcuccuaguac
gagaggaccggaguggacgcaucacugguguucggguugucaugccaaug
gcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaa
gcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccug
aaggaacguugaagacgacgacguugauaggccggguguguaagcgcagc
gaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<........>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.<<<<.....>>>>..>>..
.>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<..<<<<<..<<........
<..>....>>..>>>>>.>>...........))).....>>>>>>.>>>.
..>>>>>>><<<<<<<<..>>>>>>>>....>>>>>>..<<<<<...<<<
......<<<<<<<<....>>>>>>>>...>>>..>>>>>........>>>
>>><......<<.....<<<<<<.......>>>>>><<<<....<<<<<.
<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<.
..<<<....>>>...>>>...>>>..<<<<<........>>>>>))<<<<
<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((.
..>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>.
.>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>.
..>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>...
..<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<
<<<<<.<<...............<<<<<.....<..>......>>>>><<
<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>>.......
.....<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<..
..>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<....<..
.<<<<<..<<....>>...>>>>>..>.....>>>>>>>>..>>>>><<<
<<<.......>>>>>>........<...........<<<<<<.....>>>
>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>
>>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[.
.....<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<<
...........<<<<....<<......<<<<<<<<....>>>>>>>>...
>>..............>>>>..>>>>.>>>>>>>>>>>...<<<.<<<<<
<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>>
<<<<<<...........>>>>>>.(<<...<<<<<<<...<<<<<<....
...>>>>>>.....<<)..(((>>....>>>>>>>...<<<<..<<<<..
..>>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.((..>>
>>..))>>>>>>>.............>>>>..]]>>>>.......<<<<.
<.<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<<
<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>
>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>..
..]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<......
.........>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>
>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>
>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....>>>>><..
..<<..<<<<<.......>>>>>....<<<<<<<<..<<....<<<<<..
..>>>>>...>>...>>>>>.>>>.....>>..>..>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8syl Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): I4 K6 H7 R8 H9 R11 S13 Q15 K16 R18 R25 N40 K41 K42 K49 S53 A56 N57 H60 N61 D77 E78 P80 K83 R84 P87 R88 A89 K90 G91 R92 A93 D94 I96 L97 K98 R99 H102
• Binding residue (residue number reindexed from 1): I4 K6 H7 R8 H9 R11 S13 Q15 K16 R18 R25 N40 K41 K42 K49 S53 A56 N57 H60 N61 D77 E78 P80 K83 R84 P87 R88 A89 K90 G91 R92 A93 D94 I96 L97 K98 R99 H102

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042255 ribosome assembly
• GO:0042256 cytosolic ribosome assembly
• GO:0046677 response to antibiotic
• GO:1902626 assembly of large subunit precursor of preribosome

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:8syl, PDBe:8syl, PDBj:8syl
• PDBsum: 8syl
• PubMed: 37537169
• UniProt: P61175|RL22_ECOLI Large ribosomal subunit protein uL22 (Gene Name=rplV)