Structure of PDB 7f0d Chain Q Binding Site BS01

Receptor Information

>7f0d Chain Q (length=122) Species: 419947 (Mycobacterium tuberculosis H37Ra)

ARVKRAVNAHKKRRSILKASRGYRGQRSRLYRKAKEQQLHSLNYAYRDRR
ARKGEFRKLWIARINAAARLNDITYNRLIQGLKAAGVEVDRKNLADIAIS
DPAAFTALVDVARAALPEDVNA

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): A2 R3 V4 K5 R6 A7 N9 A10 H11 K12 K13 R14 R15 G23 Y24 R25 Q27 R28 S29 R30 L31 R33 K34 K36 E37 Q38 H41 S42 Y45 A46 Y47 R48 D49 R50 R51 R53 F57 R58 K59 W61 I62 N66 R70 Y76 N77 R78 Q81 K84 D91 R92 K93 V121 N122 A123
• Binding residue (residue number reindexed from 1): A1 R2 V3 K4 R5 A6 N8 A9 H10 K11 K12 R13 R14 G22 Y23 R24 Q26 R27 S28 R29 L30 R32 K33 K35 E36 Q37 H40 S41 Y44 A45 Y46 R47 D48 R49 R50 R52 F56 R57 K58 W60 I61 N65 R69 Y75 N76 R77 Q80 K83 D90 R91 K92 V120 N121 A122

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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: A5U300|RL20_MYCTA Large ribosomal subunit protein bL20 (Gene Name=rplT)