Structure of PDB 8buu Chain J Binding Site BS01

Receptor Information

>8buu Chain J (length=144) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

RTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDT
GDHVIIINAEKIELTGKKLTDKIYYRHTQHPGGLKSRTALEMRTNYPEKM
LELAIKGMLPKGSLGRQMFKKLNVYRGSEHPHEAQKPEVYELRG

Ligand information

>8buu Chain A (length=2852)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggauuagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacacgugaaauuccgucggaaucc
gggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaac
caguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagag
auccugaaaccgugugccuacaaguagucagagcccguuaacgggugaug
gcgugccuuuuguagaaugaaccggcgaguuacgaucccgugcaagguua
agcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcauga
guacguggucguagacccgaaaccaggugaucuacccauguccaggguga
aguucagguaacacugaauggaggcccgaacccacgcacguugaaaagug
cggggaugagguguggguaggggugaaaugccaaucgaaccuggagauag
cugguucucuccgaaauagcuuuagggcuagccucaagguaagagucuug
gagguagagcacugauuggacuaggggccgguuaccgaauucagucaaac
uccgaaugccaaugacuuauccuugggagucagacugcgagugauaagau
ccguagucgaaagggaaacagcccagaccgccagcuaaggucccaaagua
uacguuaaguggaaaaggauguggaguugcuuagacaacuggucgaguga
cucugcgccgaaaauguaccggggcuaaacguaucaccgaagcugcggac
uguucgaacagugguaggagagcguucuaagggcugugaagccagaccgg
aaggacugguggagcgcuuagaagugagaaugccgguaugaguagcgaaa
gaggggugagaauccccuccaccgaaugccuaagguuuccugaggaaggc
ucguccgcucaggguuagucgggaccuaagccgaggccgaaaggcguagg
cgauggacaacagguugauauuccuguaccaccuccucaccauuugagca
auggggggacgcaggaggauaggguaagcgcgguauuggauauccgcguc
caagcaguuaggcugggaaauaggcaaauccguuucccauaaggcugagc
ugugauggcgagcgagcgaaguuccugauuccacacugccaagaaaagcc
ucuagcgaggugagaggugcccguaccgcaaaccgacacagguaggcgag
gagagaauccuaaggugaucgagagaacucucguuaaggaacucggcaaa
augaccccguaacuucgggagaaggggugcucuguuagggugcaagcccg
agagagccgcagugaauaggcccaggcgacuguuuagcaaaaacacaggu
cucugcgaagccguaaggcgaaguauaggggcugacgccugcccggugcu
ggaagguuaagaggagcgcuuagcguaagcgaaggugcgaauugaagccc
caguaaacggcggccguaacuauaacgguccuaagguagcgaaauuccuu
gucggguaaguuccgacccgcacgaaaggcgcaacgaucugggcacuguc
ucaacgagagacucggugaaauuauaguaccugugaagaugcagguuacc
cgcgacaggacggaaagaccccguggagcuuuacugcagccugauauuga
auguugguacagcuuguacaggauagguaggagccuuggaaaccggagcg
ccagcuucgguggaggcaucggugggauacuacccuggcuguauugaccu
ucuaacccgccgcccuuaucgggcggggagacagugucaggugggcaguu
ugacuggggcggucgccuccuaaaagguaacggaggcgcccaaagguucc
cucagaaugguuggaaaucauucgcagaguguaaaggcacaagggagcuu
gacugcgagaccuacaagucgagcagggacgaaagucgggcuuagugauc
cggugguuccgcauggaagggccaucgcucaacggauaaaagcuaccccg
gggauaacaggcuuaucucccccaagaguccacaucgacggggagguuug
gcaccucgaugucggcucaucgcauccuggggcuguagucagucccaagg
guugggcuguucgcccauuaaagcgguacgcgagcuggguucagaacguc
gugagacaguucggucccuauccgucgcgggcgcaggaaauuugagagga
gcuguccuuaguacgagaggaccgggauggacgcaccgcugguguaccag
uuguucugccaagggcaucgcuggguagcuaugugcggacgggauaagug
cugaaagcaucuaagcaugaagccccccucaagaugagauuucccauucc
gcaaggaaguaagaucccugaaagaugaucagguugauaggucugaggug
gaaguguggcgacacauggagcugacagauacuaaucgaucgaggacuua
ac

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8buu Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R2 T4 N8 W16 G27 R28 S31 R38 K40 H48 H54 T66 G67 K68 K69 K73 Y76 R77 H78 T79 Q80 H81 P82 G83 L85 R88 K100 E103 A105 G108 M109 K112 S114 L115 R117 K121 H133 A135 Q136 K137 G145
• Binding residue (residue number reindexed from 1): R1 T3 N7 W15 G26 R27 S30 R37 K39 H47 H53 T65 G66 K67 K68 K72 Y75 R76 H77 T78 Q79 H80 P81 G82 L84 R87 K99 E102 A104 G107 M108 K111 S113 L114 R116 K120 H132 A134 Q135 K136 G144

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

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

External links

• PDB: RCSB:8buu, PDBe:8buu, PDBj:8buu
• PDBsum: 8buu
• PubMed: 36951104
• UniProt: P70974|RL13_BACSU Large ribosomal subunit protein uL13 (Gene Name=rplM)