Structure of PDB 8kab Chain M Binding Site BS01

Receptor Information

>8kab Chain M (length=145) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

VIKLHDLKPAPGEKKAKTRVGRGEGSKGKTAGRGTKGTKARKNVPVMFEG
GQMPIHMRLPKLKGFKNRFRTEYQVVNVGDINKAFPQGGTVGVDELVAKG
LVRKNSLVKVLGDGKLTVKVDVTANKFSGSAREAITAAGGSATEL

Ligand information

>8kab Chain A (length=3111)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucuaccuggcuggag
ggcagugagaaaauguugugguuagcggaaauggcuugggauggccugcc
guagacggugagagcccgguacgugaaaacccgacgucugucuugauggu
guucccgaguagcagcgggcccguggaaucugcugugaaucugccgggac
cacccgguaagccugaauacuucccagugaccgauagcggauuaguaccg
ugagggaauggugaaaaguaccccgggaggggagugaaagaguaccugaa
accgugcgcuuacaauccgucagagcccucgacgugucguggggugaugg
cgugccuuuugaagaaugagccugcgagucagggacaugucgcgagguua
acccgggugggguagccgcagcgaaagcgagucugaauagggcguaucca
cacaagagugugugguguagugguguguucuggacccgaagcggagugau
cuacccauggccagggugaagcgcggguaagaccgcguggaggcccgaac
ccacuuagguugaagacugaggggaugagcuguggguaggggugaaaggc
caaucaaacuccgugauagcugguucuccccgaaaugcauuuaggugcag
cgucgcauguuucuugccggagguagagcuacuggauggccgaugggccc
cacaggguuacugacgucagccaaacuccgaaugccgguaaguccaagag
ugcggcagugagacggcgggggauaagcuccgugcgucgagagggaaaca
gcccagaucgccggcuaaggccccuaagcgugugcuaaguggaaaaggau
gugcagucgcgaagacaaccaggagguuggcuuagaagcagccacccuug
aaagagugcguaauagcucacuggucaagugauugugcgccgauaaugua
gcggggcucaagcacaccgccgaagccgcggcagccaacguguuggcugg
guaggggagcguccugcauccggugaagccgccgagugaucgaguggugg
agggugugggagugagaaugcaggcaugaguagcgauuaggcaagugaga
accuugcccgccgaaagaccaaggguuccugggccaggccaguccgccca
gggugagucgggaccuaaggcgaggccgacaggcguagucgauggacaac
ggguugauauucccguacccguguaugugcguccaugaugaaucagcggu
acuaaccauccaaaaccaccgugaccgcaccuuucgggguguggcguugg
uggggcugcaugggaccuucguugguaguagucaagcgauggggugacgc
aggaagguagccguaccggucagugguaauaccgggguaagccuguaggg
agucagauagguaaauccgucuggcauauauccugagaggugaugcauag
ccgagugaggcgaauucggugauccuaugcugccgagaaaagccucuagc
gaggacauacacggcccguaccccaaaccaacacagguggucagguagag
aauacuaaggcguacgagugaacuaugguuaaggaacucggcaaaaugcc
cccguaacuucgggagaagggggacccacauggcguguaagccuuuacgg
cccaagcgugaguggguggcacaaaccagugagaagcgacuguuuacuaa
aaacacagguccgugcgaagucgcaagacgauguauacggacugacgccu
gcccggugcuggaagguuaagaggacccguuaacucccuuugggggugaa
gcggagaauuuaagccccaguaaacggcggugguacauccuaagguagcg
aaauuccuugucggguaaguuccgaccugcacgaauggcguaacgacuuc
ucaacugucucaaccauagacucggcgaaauugcacuacgaguaaagaug
cucguuacgcgcggcaggacgaaaagaccccgggaccuucacuacaacuu
gguauuggugcucgauacgguuuguguaggauaggugggagacugugaag
cucacacgccaguguggguggagucguuguugaaauaccacucugaucgu
auugggccucuaaccucggaccguauauccgguucagggacagugccugg
uggguaguuuaacuggggcgguugccuccuaaaauguaacggaggcgccc
aaagguucccucaaccuggacggcaaucagguguugaguguaagugcaca
agggagcuugacugcgagacggacaugucgagcagggacgaaagucggga
cuagugauccggcaccucugaguggaaggggugucgcucaacggauaaaa
gguaccccggggauaacaggcugaucuuccccaagaguccauaucgacgg
gaugguuuggcaccucgaugucggcucgucgcauccuggggcuggagcag
gucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguu
uagaacgucgugagacaguucggucucuauccgccgcgcgcgucagaagc
uugaggaaaccugucccuaguacgagaggaccgggacggacgaaccucug
guauaccaguugucccaccaggggcacggcuggauagccacguucggaca
ggauaaccgcugaaagcaucuaagcgggaaaccucuuccaagaccaggcu
ucucacccucuaggagggauaaggccccccgcagaccacgggauugauag
accagaccuggaagccuaguaauaggugcagggaacuggcacuaaccggc
cgaaaacuuac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8kab Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): H7 K10 E15 K16 K17 K19 T20 R21 V22 G23 R24 G25 G27 S28 G30 K31 A33 G34 R35 G36 T37 K38 T40 K41 R43 K44 F50 E51 G52 G53 Q54 M55 M59 R60 L61 P62 K63 K65 G66 F67 N69 R70 F71 R72 V77 N79 R105 K111 L113 G114 D115 S130 G131 S132
• Binding residue (residue number reindexed from 1): H5 K8 E13 K14 K15 K17 T18 R19 V20 G21 R22 G23 G25 S26 G28 K29 A31 G32 R33 G34 T35 K36 T38 K39 R41 K42 F48 E49 G50 G51 Q52 M53 M57 R58 L59 P60 K61 K63 G64 F65 N67 R68 F69 R70 V75 N77 R103 K109 L111 G112 D113 S128 G129 S130

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8kab, PDBe:8kab, PDBj:8kab
• PDBsum: 8kab
• PubMed: 39029461
• UniProt: A0QSG8