Structure of PDB 8cgv Chain 1 Binding Site BS01

Receptor Information

>8cgv Chain 1 (length=46) Species: 679895 (Escherichia coli BW25113)

MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Ligand information

>8cgv Chain a (length=2687)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaaggucuaacuggaggaccgaaccgacuaauguugaaaaauuagcg
gaugacuuguggcugggggugaaaggccaaucaaaccgggagauagcugg
uucuccccgaaagcuauuuagguagcgccucgugaauucaucuccggggg
uagagcacuguuucggcaacccgaugcaaacugcgaauaccggagaaugu
uaucacgggagacacacggcgggugcuaacguccgucgugaagagggaaa
caacccagaccgccagcuaaggucccaaagucaugguuaagugggaaacg
augugggaaggcccagacagcgucgagucggccugcgcggaagauguaac
ggggcuaaaccaugcaccgaagcugcggcagcgacgcgcguuguugggua
ggggagcguucuguaagccugcgaaggugugcugugaggcaugcuggagg
uaucagaagugcgaaugcugacauaaguaacgauaaagcgggugaaaagc
ccgcucgccggaagaccaaggguuccuguccaacguuaaucggggcaggg
ugagucgaccccuaaggcgaggccgaaaggcguagucgaugggaaacagg
uuaauauuccuguacuugguguuacugcgaaggggggacggagaaggcua
uguuggccgggcgacgguugucccgguuuaagcguguaggcugguuuucc
aggcaaauccggaaaaucaaggcugaggcgugaugacgaggcacuacggu
gcugaagcaacaaaugcccugcuuccaggaaaagccucuaagcaucaggu
aacaucaaaucguaccccaaaccgacacagguggucagguagagaauacc
aaggcgcuugagagaacucgggugaaggaacuaggcaaaauggugccgua
acuucgggagaaggcacgcugauauguaggugaggucccucgcggaugga
gcugaaaucagucgaagauaccagcuggcugcaacuguuuauuaaaaaca
cagcacugugcaaacacgaaaguggacguauacggugugacgccugcccg
gugccggaagguuaauugaugggguuagcgcaagcgaagcucuugaucga
agccccgguaaacggcguaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaauggcguaaugauggccaggcugucuccacccgagacuc
agugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgga
aagaccccgugaaccuuuacuauagcuugacacugaacauauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
agguuagugcaauggcauaagccagcuugacugcgagcgugacggcgcga
gcaggugcgaaagcaggucauagugauccggugguucugaauggaagggc
caucgcucaacggauaaaagguacuccggggauaacaggcugauaccgcc
caagaguucauaucgacggcgguguuuggcaccucgaugucggcucauca
cauccuggggcugaaguaggucccaaggguauggcuguucgccauuuaaa
gugguacgcgagcuggguuuagaacgucgugagacaguucggucccuauc
ugccgugggcgcuggagaacugaggggggcugcuccuaguacgagaggac
cggaguggacgcaucacugguguucggguugucaugccaauggcacugcc
cgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaa
cuugccccgagaugaguucucccugacccuuuaaggguccugaaggaacg
uugaagacgacgacguugauaggccggguguguaagcgcagcgaugcguu
gagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cgv Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 1.66 Å
• Binding residue (original residue number in PDB): M1 K2 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 N13 R14 S15 H16 F18 R19 R21 M22 K25 N26 Q29 R33 R34 R35 K37 G38 R39 A40 R41 S45 K46
• Binding residue (residue number reindexed from 1): M1 K2 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 N13 R14 S15 H16 F18 R19 R21 M22 K25 N26 Q29 R33 R34 R35 K37 G38 R39 A40 R41 S45 K46

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• 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:8cgv, PDBe:8cgv, PDBj:8cgv
• PDBsum: 8cgv
• PubMed: 37550453
• UniProt: P0A7P5|RL34_ECOLI Large ribosomal subunit protein bL34 (Gene Name=rpmH)