Structure of PDB 7f0d Chain V Binding Site BS01

Receptor Information
>7f0d Chain V (length=177) Species: 419947 (Mycobacterium tuberculosis H37Ra) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNQLRVTVRTETGKGASRRARRAGKIPAVLYGHGAEPQHLELPGHDYAAV
LRHSGTNAVLTLDIAGKEQLALTKALHIHPIRRTIQHADLLVVRRGEKVV
VEVSVVVEGQAGPDTLVTQETNSIEIEAEALSIPEQLTVSIEGAEPGTQL
TAGQIALPAGVSLISDPDLLVVNVVKA
Ligand information
>7f0d Chain A (length=3118) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aagugucuaagggcgcaugguggaugccuuggcaucgagagccgaugaag
gacgugggaggcugcgauaugccucggggagcugucaaccgagcguggau
ccgaggauuuccgaauggggaaacccagcacgagugaugucgugcuaccc
gcaucugaauauauagggugcgggagggaacgcggggaagugaaacaucu
caguacccguaggaggagaaaacaauugugauuccgcaaguaguggcgag
cgaacgcggaacaggcuaaaccgcacgcauggguaaccggguagggguug
ugugugcgggguugugggaggauaugucucagcgcuacccggcugagagg
cagucagaaagugucgugguuagcggaaguggccugggauggucugccgu
agacggugagagcccgguacgcgaaaacccggcaccugccuaguaucaau
ucccgaguagcagcgggcccguggaauccgcugugaauccgccgggacca
cccgguaagccuaaauacuccucgaugaccgauagcggauuaguaccgug
agggaauggugaaaaguaccccgggaggggagugaaagaguaccugaaac
cgugugccuacaauccgucagagccuccuuuuccucuccggaggagggug
gugauggcgugccuuuugaagaaugagccugcgagucagggacaugucgc
aagguuaacccgugugggguagccgcagcgaaagcgagucugaauagggc
gacccacacgcgcauacgcgcgugugaauaguggcguguucuggacccga
agcggagugaucuacccauggccagggugaagcgcggguaagaccgcgug
gaggcccgaacccacuuagguugaagacugaggggaugagcuguggguag
gggugaaaggccaaucaaacuccgugauagcugguucuccccgaaaugca
uuuaggugcagcguugcgugguucaccgcggagguagagcuacuggaugg
ccgauggguuacugacgucagccaaacuccgaaugccgugguguaaagcg
uggcagugagacggcgggggauaagcuccguacgucgaaagggaaacagc
ccagaucgccggcuaaggcccccaagcgugugcuaagugggaaaggaugu
gcagucgcaaagacaaccaggagguuggcuuagaagcagccacccuugaa
agagugcguaauagcucacuggucaagugauugugcgccgauaauguagc
ggggcucaagcacaccgccgaagccgcggcacauccaccuuguggugggu
guggguaggggagcgucccucauucagcgaagccaccgggugaccggugg
uggagggugggggagugagaaugcaggcaugaguagcgacaaggcaagug
agaaccuugcccgccgaaagaccaaggguuccugggccaggccaguccgc
ccagggugagucgggaccuaaggcgaggccgacaggcguagucgauggac
aacggguugauauucccguacccgugugugggcgcccgugacgaaucagc
gguacuaaccacccaaaaccggaucgaucacuccccuucgggggugugga
guucuggggcugcgugggaacuucgcugguaguagucaagcgaaggggug
acgcaggaagguagccguaccagucagugguaacacuggggcaagccggu
agggagagcgauaggcaaauccgucgcucacuaauccugagaggugacgc
auagccgguugaggcgaauucggugauccucugcugccaagaaaagccuc
uagcgagcacacacacggcccguaccccaaaccgacacagguggucaggu
agagcauaccaaggcguacgagauaacuaugguuaaggaacucggcaaaa
ugcccccguaacuucgggagaagggggaccggaauaucgugaacacccuu
gcggugggagcgggauccggucgcagaaaccagugaggagcgacuguuua
cuaaaaacacagguccgugcgaagucgcaagacgauguauacggacugac
gccugcccggugcuggaagguuaagaggacccguuaacccgcaaggguga
agcggagaauuuaagccccaguaaacggcggugguaacuauaaccauccu
aagguagcgaaauuccuugucggguaaguuccgaccugcacgaauggcgu
aacgacuucucaacugucucaaccauagacucggcgaaauugcacuacga
guaaagaugcucguuacgcgcggcaggacgaaaagaccccgggaccuuca
cuacaacuugguauugauguucgguacgguuuguguaggauaggugggag
acugugaaaccucgacgccaguuggggcggagucguuguugaaauaccac
ucugaucguauugggcaucuaaccucgaacccugaaucggguuuagggac
agugccuggcggguaguuuaacuggggcgguugccuccuaaaauguaacg
gaggcgcccaaagguucccucaaccuggacggcaaucagguggcgagugu
aaaugcacaagggagcuugacugcgagacuuacaagucaagcagggacga
aagucgggauuagugauccggcacccccgaguggaaggggugucgcucaa
cggauaaaagguaccccggggauaacaggcugaucuuccccaagagucca
uaucgacgggaugguuuggcaccucgaugucggcucgucgcauccugggg
cuggagcaggucccaaggguugggcuguucgcccauuaaagcggcacgcg
agcuggguuuagaacgucgugagacaguucggucucuauccgccgcgcgc
gucagaaacuugaggaaaccugucccuaguacgagaggaccgggacggac
gaaccucuggugcaccaguugucccgccaggggcaccgcuggauagccac
guucggucaggauaaccgcugaaagcaucuaagcgggaaaccuucuccaa
gaucagguuucucacccacuuggugggauaaggccccccgcagaacacgg
guucaauaggucagaccuggaagcucaguaauggguguagggaacuggug
cuaaccggccgaaaacuu
<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<<......<
<<<<<.((..((.>>>.....<<<<<<<..<<<))...)).>>>.....>
>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<<
<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>.
.....>>>>>.>...[.....<<....>>..<<<<<<.....<<.....>
>....>>>>>>..<<<....<<<<<<<<<<........(((........>
>>>>>>>>>......<<<<<<<<<..<<<<<<<....))).>>>>>>><<
<<........<<<<<..<<<<.<<<.....<<<<......>>>>.((...
...<<<.....))>>>...>>>...>>>>.>>>>>.>>>>...>>>>..>
>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<<<
<>>>>>..>>>....].>>.>>>>>>>.>>...............<<...
.>>....>>.........<<<<....>>>>..................>>
>>>>>>>>>.......<<<<..<<<.<<<<<.<.......>..>>>>>.>
>>..>>>>...<.<........>.>.<<<<<<....<<<.<<<<<<<<<<
..<<<...<<<<..>>>>...>>>...<<....>>..<<<<.....>>>>
.....<<<<<<<<....>>>>>>>>.....>>>>>>>>>>>>>..<<.<.
.<<<<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>>>.
....>>>...<<<.<<<<<........>>>>>>>>....>>>>>>>>>..
.<<<.....>>>......>>>>>>...>..>.>>..<<<<<<....<<<<
<....>>>>><<<<<<<<<....<<<<<<<<.....<<<....<<<.<<<
<...............>>>>.>>>..>>.>.....>>>>>>>>....>>>
>>>>.>>..<<<<<<<<<<......>>>>>>.>>>>....<<<......>
>>...<<<<.<<<...<<<(((.....<<<<<<...........<<..<<
<<<<<<<........<<<<<.<<...<<<.........>>>...>>....
.....<<......>>...>>>>>....>>>>>>>>>.>>...........
)))......>>>>>>.>>>...>>>>>>><<<<<<<<<<....>>>>>>>
>>>....>>>>>>..<<<<<<<<<.......<<<<<<<<....>>>>>>>
>....>>>>>>>>>........>>>>>><......<<.....<<<<<<..
.....>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>
>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...>>..
.<<<<<........>>>>>))<<<<<<<<<.<<.....<<<<...<<<<<
<<.<....<<<<.<<...<<<<<....<<<..<<<<...>>.>>..>>>.
..>>>>>...>>.>>>>....>>>>>>>>.....>>>>.<<..<<<<<<.
..<<<<..<<<..<<<<..<<<<<...((((...>>>>>.<<..<<<...
.<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>....>>>...>>
...<<........>>.....>>>>...>>>...>>>>........>>>>>
>.>>..>>.>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<
<.....>>>>..>>>>..<<<<....<<<<<<<<.<<.........<...
..<<<<<...............>>>>><<<<<....<<......<<<...
..>>>.......>.>.>>>>>............<<<<<<<<<..<<<...
......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<
<<<.<<<..<<<<<<<..<<<<.<<<....<<<<<.<<<<....>>>>>.
.>>>>....>>>.>>>>>>>>>..>>>>><<<<<.........>>>>>..
......<...........<<<<<<.....>>>>>>.....>....>>>>>
..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.((..<<<<
<......))>>>>>..<<<<<<<<.<<<.<<......<<<<<<<<<<..<
<<<<..<<.<<<<<.<<<<<<<.<<<<<<.....................
..................................................
.....>>>>>>.>>>>>>>...<<<.<<<<<........>>>>>>>>...
.>>>>>.>>...>>>>>..<<<<.....>>>><<<<<<...........>
>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[
.(((>>....>>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<..
..>>>.>>)))]......<<<<<<<.<<..>>>>..>>>>>>>>>.....
........>>>>..>>>>>>.......<<<<..<<.<<<<...<<.....
..>>...>>>>.>>...>>>.>.......<.<<<.<<<<<<..<<<<<<<
<<......>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>..>..
.>>>..>....<<<<<<<....>>>.>>>>....>>..>>>>>>>>>>>.
...<<<<<<<...<<<...<<<<<<<...............>>>>>>>.<
<<<<...<<<<...<<<<<<<<<<<))))>>>>>>..>>>>>...>>>>.
>>>>>...<<<....<<<<<...........>>>>>....>>>..>>>..
.....>>>>>>>..<<<<<...>>>>>....<<<<.<<<<.......>>>
>.....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.
>>>...>>>>....>>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7f0d Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		R57 E125 Q154 L175 N178
Binding residue
(residue number reindexed from 1)		R52 E120 Q149 L170 N173
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7f0d, PDBe:7f0d, PDBj:7f0d
PDBsum7f0d
PubMed34935599
UniProtA5U158

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