Structure of PDB 8ifc Chain g Binding Site BS01

Receptor Information

>8ifc Chain g (length=176) Species: 562 (Escherichia coli)

SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLT
FGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGN
VINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAY
RRPEPYKGKGVRYADEVVRTKEAKKK

Ligand information

>8ifc Chain a (length=2753)

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
aagaccccgugaaccuuuacuauagcuugacacugaacauauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ifc Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): S2 R3 N38 A63 Q64 G66 T67 A70 F109 S110 H111 Q139 G142 Q143 P156 Y157 K160 K172 K175
• Binding residue (residue number reindexed from 1): S1 R2 N37 A62 Q63 G65 T66 A69 F108 S109 H110 Q138 G141 Q142 P155 Y156 K159 K171 K174

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

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:8ifc, PDBe:8ifc, PDBj:8ifc
• PDBsum: 8ifc
• PubMed: 38227611
• UniProt: P0AG55|RL6_ECOLI Large ribosomal subunit protein uL6 (Gene Name=rplF)