Structure of PDB 8ifb Chain s Binding Site BS01

Receptor Information

>8ifb Chain s (length=93) Species: 562 (Escherichia coli)

MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKL
FEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNL

Ligand information

>8ifb 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: 8ifb Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
• Resolution: 2.43 Å
• Binding residue (original residue number in PDB): M1 H15 S17 K19 T39 K40 N59 T60 L61 V62 K64 K66 K68 R69 H70 R73 R76 R77 S78 K81 K82 Y84
• Binding residue (residue number reindexed from 1): M1 H15 S17 K19 T39 K40 N59 T60 L61 V62 K64 K66 K68 R69 H70 R73 R76 R77 S78 K81 K82 Y84

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein 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:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ifb, PDBe:8ifb, PDBj:8ifb
• PDBsum: 8ifb
• PubMed: 38227611
• UniProt: P0ADZ0|RL23_ECOLI Large ribosomal subunit protein uL23 (Gene Name=rplW)