Structure of PDB 7f0d Chain M Binding Site BS01

Receptor Information

>7f0d Chain M (length=134) Species: 419947 (Mycobacterium tuberculosis H37Ra)

LIPRKVKHRKQHHPRQRGIASGGTTVNFGDYGIQALEHAYVTNRQIESAR
IAINRHIKRGGKVWINIFPDRPLTKKPAETRMGSGKGSPEWWVANVKPGR
VLFELSYPNEGVARAALTRAIHKLPIKARIITRE

Ligand information

>7f0d Chain A (length=3118)

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

Structure summary

• PDB: 7f0d Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): P4 R5 H9 K11 Q12 H13 H14 R16 Q17 G24 A40 Y41 R45 Q46 S49 K63 W65 F69 T75 K77 E80 R82 M83 G84 G86 G88 R101 R120 H123 K124 P126 K128
• Binding residue (residue number reindexed from 1): P3 R4 H8 K10 Q11 H12 H13 R15 Q16 G23 A39 Y40 R44 Q45 S48 K62 W64 F68 T74 K76 E79 R81 M82 G83 G85 G87 R100 R119 H122 K123 P125 K127

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7f0d, PDBe:7f0d, PDBj:7f0d
• PDBsum: 7f0d
• PubMed: 34935599
• UniProt: A5U094|RL16_MYCTA Large ribosomal subunit protein uL16 (Gene Name=rplP)