Structure of PDB 8bge Chain J Binding Site BS01

Receptor Information

>8bge Chain J (length=136) Species: 83333 (Escherichia coli K-12)

MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAAR
RAMTRAVKRQGKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGK
VLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM

Ligand information

>8bge Chain 0 (length=2758)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggcuuaccaacccgaugca
aacugcgaauaccggagaauguuaucacgggagacacacggcgggugcua
acguccgucgugaagagggaaacaacccagaccgccagcuaaggucccaa
agucaugguuaagugggaaacgaugugggaaggcccagacagccgagucg
gccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggca
gcgacgcuuaugcguuguuggguaggggagcguucuguaagccugcgaag
gugugcugugaggcaugcuggagguaucagaagugcgaaugcugacauaa
guaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguucc
uguccaacguuaaucggggcagggugagucgaccccuaaggcgaggccga
aaggcguagucgaugggaaacagguuaauauuccuguacuugguguuacu
gcgaaggggggacggagaaggcuauguuggccgggcgacgguugucccgg
uuuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcuga
ggcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcuucc
aggaaaagccucuaagcaucagguaacaucaaaucguaccccaaaccgac
acagguggucagguagagaauaccaaggcgcuugagagaacucgggugaa
ggaacuaggcaaaauggugccguaacuucgggagaaggcacgcugauaug
uaggugaggucccucgcggauggagcugaaaucagucgaagauaccagcu
ggcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaagugga
cguauacggugugacgccugcccggugccggaagguuaauugaugggguu
agcgcaagcgaagcucuugaucgaagccccgguaaacggcggccguaacu
auaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccugc
acgaauggcguaaugauggccaggcugucuccacccgagacucagugaaa
uugaacucgcugugaagaugcaguguacccgcggcaagacggaaagaccc
cgugaaccuuuacuauagcuugacacugaacauugagccuguuugauguu
cuaacguugacccguaauccggguugcggacagugucugguggguaguuu
gacuggggcggucuccuccuaaagaguaacggaggagcacgaagguuggc
uaauccuggucggacaucaggagguuagugcaauggcauaagccagcuug
acugcgagcgugacggcgcgagcaggugcgaaagcaggucauagugaucc
ggugguucugaauggaagggccaucgcucaacggauaaaagguacuccgg
ggauaacaggcugauaccgcccaagaguucauaucgacggcgguguuugg
caccucgaugucggcucaucacauccuggggcugaaguaggucccaaggg
uauggcuguucgccauuuaaagugguacgcgagcuggguuuagaacgucg
ugagacaguucggucccuaucugccgugggcgcuggagaacugagggggg
cugcuccuaguacgagaggaccggaguggacgcaucacugguguucgggu
ugucaugccaauggcacugcccgguagcuaaaugcggaagagauaagugc
ugaaagcaucuaagcacgaaacuugccccgagaugaguucucccugaccc
uuuaaggguccugaaggaacguugaagacgacgacguugauaggccgggu
guguaagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugagg
cuuaaccu

<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<.))).....>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<.....<<<.<<<<...<<<<..>>.>>...>>>>.>>>
.....>.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<....
..>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((..
...<<<<<<...........<<..<<<<<..<<..............>>.
.>>>>>.>>...........))).....>>>>>>.>>>...>>>>>>><<
<<<<<<<....>>>>>>>>>....>>>>>><.<<<<<...<<<......<
<<<<<<<....>>>>>>>>...>>>..>>>>>..>.....>>>>>><...
...<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<
<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<...<<<..
..>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<
<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>
><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>..
.>>>>...>><..<<<<<<..>>>>>>...>>>>>>...>>>...>>>.>
........>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<
<...............<<<<<.....<..>......>>>>><<<<<<...
..<<<...<<<<.....>>>>...>>>...>>>>>>............<<
<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>..
.....>>>>>>>.<<<<<.<<<..<<<<<<<..<<<<.......<<<<<<
.<<....>>..>>>>>>.......>>>>>>>>>..>>>>><<<<<<....
...>>>>>>........<...........<<<<<.......>>>>>....
.>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>....
.>.....<<<<<........>>>>>..<<<<<<<<.(((.[[......<<
<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<..>>>>>>>>>>
>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..
<<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<
...<<<<<<.......>>>>>>.....<<...(((>>....>>>>>>>..
.<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>))).......<
<<<<<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>
>.......<<<<...<<<<<<...<<.......>>...>>>>>>....>>
>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>
.<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<.
...>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..
<<<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<
<<<<<.)))..>>>>>..>>>>>...>>>>.>>>>>...<<<.<..<<<<
<...........>>>>>...>>>>.>>>>.......>>>>>>>..<<<<<
.....>>>>><....<<..<<<<<.......>>>>>....<<<<<<<<..
<<....<<<<<....>>>>>...>>...>>>>>.>>>.....>>..>..>
>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bge Modulation of translational decoding by m 6 A modification of mRNA.
• Resolution: 2.11 Å
• Binding residue (original residue number in PDB): K5 R6 K8 F9 H13 K14 R44 Q45 K62 W64 F68 L78 R81 M82 G83 K84 G85 K86 A122 K123 P125
• Binding residue (residue number reindexed from 1): K5 R6 K8 F9 H13 K14 R44 Q45 K62 W64 F68 L78 R81 M82 G83 K84 G85 K86 A122 K123 P125

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• 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:8bge, PDBe:8bge, PDBj:8bge
• PDBsum: 8bge
• PubMed: 37553384
• UniProt: P0ADY7|RL16_ECOLI Large ribosomal subunit protein uL16 (Gene Name=rplP)