Structure of PDB 6hrm Chain S Binding Site BS01

Receptor Information

>6hrm Chain S (length=110) Species: 562 (Escherichia coli)

METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKV
LESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRT
SHITVVVSDR

Ligand information

>6hrm Chain 1 (length=4450)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccg
gucaacagccguuugagcuaaccgguacuaaugaaccgugaggcuuaacc
uugagagguuaagcgacuaagcguacacgguggaugcccuggcagucaga
ggcgaugaaggacgugcuaaucugcgauaagcgucgguaaggugauauga
accguuauaaccggcgauuuccgaauggggaaacccaguguguuucgaca
cacuaucauuaacugaauccauagguuaaugaggcgaaccgggggaacug
aaacaucuaaguaccccgaggaaaagaaaucaaccgagauucccccagua
gcggcgagcgaacggggagcagcccagagccugaaucaguguguguguua
guggaagcgucuggaaaggcgcgcgauacagggugacagccccguacaca
aaaaugcacaugcugugagcucgaugaguagggcgggacacgugguaucc
ugucugaauauggggggaccauccuccaaggcuaaauacuccugacugac
cgauagugaaccaguaccgugagggaaaggcgaaaagaaccccggcgagg
ggagugaaaaagaaccugaaaccguguacguacaagcagugggagcacgc
uuaggcgugugacugcguaccuuuuguauaaugggucagcgacuuauauu
cuguagcaagguuaaccgaauaggggagccgaagggaaaccgagucuuaa
cugggcguuaaguugcaggguauagacccgaaacccggugaucuagccau
gggcagguugaagguuggguaacacuaacuggaggaccgaaccgacuaau
guugaaaaauuagcggaugacuuguggcugggggugaaaggccaaucaaa
ccgggagauagcugguucuccccgaaagcuauuuagguagcgccucguga
auucaucuccggggguagagcacuguuucggcaagggggucaucccgacu
uaccaacccgaugcaaacugcgaauaccggagaauguuaucacgggagac
acacggcgggugcuaacguccgucgugaagagggaaacaacccagaccgc
cagcuaaggucccaaagucaugguuaagugggaaacgaugugggaaggcc
cagacagccaggauguuggcuuagaagcagccaucauuuaaagaaagcgu
aauagcucacuggucgagucggccugcgcggaagauguaacggggcuaaa
ccaugcaccgaagcugcggcagcgacgcuuaugcguuguuggguagggga
gcguucuguaagccugcgaaggugugcugugaggcaugcuggagguauca
gaagugcgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcu
cgccggaagaccaaggguuccuguccaacguuaaucggggcagggugagu
cgaccccuaaggcgaggccgaaaggcguagucgaugggaaacagguuaau
auuccuguacuugguguuacugcgaaggggggacggagaaggcuauguug
gccgggcgacgguugucccgguuuaagcguguaggcugguuuuccaggca
aauccggaaaaucaaggcugaggcgugaugacgaggcacuacggugcuga
agcaacaaaugcccugcuuccaggaaaagccucuaagcaucagguaacau
caaaucguaccccaaaccgacacagguggucagguagagaauaccaaggc
gcuugagagaacucgggugaaggaacuaggcaaaauggugccguaacuuc
gggagaaggcacgcugauauguaggugaggucccucgcggauggagcuga
aaucagucgaagauaccagcuggcugcaacuguuuauuaaaaacacagca
cugugcaaacacgaaaguggacguauacggugugacgccugcccggugcc
ggaagguuaauugaugggguuagcgcaagcgaagcucuugaucgaagccc
cgguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccuu
gucggguaaguuccgaccugcacgaauggcguaaugauggccaggcuguc
uccacccgagacucagugaaauugaacucgcugugaagaugcaguguacc
cgcggcaagacggaaagaccccgugaaccuuuacuauagcuugacacuga
acauugagccuugauguguaggauaggugggaggcuuugaaguguggacg
ccagucugcauggagccgaccuugaaauaccacccuuuaauguuugaugu
ucuaacguugacccguaauccggguugcggacagugucugguggguaguu
ugacuggggcggucuccuccuaaagaguaacggaggagcacgaagguugg
cuaauccuggucggacaucaggagguuagugcaauggcauaagccagcuu
gacugcgagcgugacggcgcgagcaggugcgaaagcaggucauagugauc
cggugguucugaauggaagggccaucgcucaacggauaaaagguacuccg
gggauaacaggcugauaccgcccaagaguucauaucgacggcgguguuug
gcaccucgaugucggcucaucacauccuggggcugaaguaggucccaagg
guauggcuguucgccauuuaaagugguacgcgagcuggguuuagaacguc
gugagacaguucggucccuaucugccgugggcgcuggagaacugaggggg
gcugcuccuaguacgagaggaccggaguggacgcaucacugguguucggg
uugucaugccaauggcacugcccgguagcuaaaugcggaagagauaagug
cugaaagcaucuaagcacgaaacuugccccgagaugaguucucccugacc
cuuuaaggguccugaaggaacguugaagacgacgacguugauaggccggg
uguguaaacggacaugguuggagggcgcuuaccacuuugugauucaugac
uggggugaagucguaacaagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hrm Controlling orthogonal ribosome subunit interactions enables evolution of new function.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): I4 K6 H7 R8 H9 S13 Q15 K16 R18 R25 K41 K42 K49 A56 N57 H60 N61 D77 E78 R84 M86 P87 R88 A89 K90 G91 R92 A93 D94 R95 I96 L97 K98
• Binding residue (residue number reindexed from 1): I4 K6 H7 R8 H9 S13 Q15 K16 R18 R25 K41 K42 K49 A56 N57 H60 N61 D77 E78 R84 M86 P87 R88 A89 K90 G91 R92 A93 D94 R95 I96 L97 K98

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042255 ribosome assembly
• GO:0042256 cytosolic ribosome assembly
• GO:0046677 response to antibiotic
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6hrm, PDBe:6hrm, PDBj:6hrm
• PDBsum: 6hrm
• PubMed: 30518861
• UniProt: P61175|RL22_ECOLI Large ribosomal subunit protein uL22 (Gene Name=rplV)