Structure of PDB 8bh4 Chain D Binding Site BS01

Receptor Information

>8bh4 Chain D (length=177) Species: 83333 (Escherichia coli K-12)

AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFR

Ligand information

>8bh4 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: 8bh4 Modulation of translational decoding by m 6 A modification of mRNA.
• Resolution: 2.62 Å
• Binding residue (original residue number in PDB): N37 M38 G39 V40 G41 T68 R71 K72 F77 K88 S121 D123 S129 G151 L152
• Binding residue (residue number reindexed from 1): N36 M37 G38 V39 G40 T67 R70 K71 F76 K87 S120 D122 S128 G150 L151

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:8bh4, PDBe:8bh4, PDBj:8bh4
• PDBsum: 8bh4
• PubMed: 37553384
• UniProt: P62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)