Structure of PDB 8cgv Chain s Binding Site BS01

Receptor Information

>8cgv Chain s (length=91) Species: 679895 (Escherichia coli BW25113)

MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKL
FEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQ

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 R3 H15 S17 E18 K19 T39 K40 N59 T60 L61 V62 K64 K66 K68 H70 R73 G75 R76 R77 S78 K81 K82 Y84
• Binding residue (residue number reindexed from 1): M1 R3 H15 S17 E18 K19 T39 K40 N59 T60 L61 V62 K64 K66 K68 H70 R73 G75 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:8cgv, PDBe:8cgv, PDBj:8cgv
• PDBsum: 8cgv
• PubMed: 37550453
• UniProt: P0ADZ0|RL23_ECOLI Large ribosomal subunit protein uL23 (Gene Name=rplW)