Structure of PDB 8b0x Chain L Binding Site BS01

Receptor Information

>8b0x Chain L (length=123) Species: 37762 (Escherichia coli B)

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRK
VCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGA
LDCSGVKDRKQARSKYGVKRPKA

Ligand information

>8b0x Chain A (length=1500)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaauucgcugacgaguggcggacggg
ugaguaaugucugggaaacugccugauggagggggauaacuacuggaaac
gguagcuaauaccgcauaacgucgcaagaccaaagagggggccucuugcc
aucggaugugcccagaugggauuagcuaguaggugggguaacggcucacc
uaggcgacgaucccuagcuggucugagaggaugaccagccacacuggaac
ugagacacgguccagacuccuacgggaggcagcaguggggaauauugcac
aaugggcgcaagccugaugcagccaugccgcguguaugaagaaggccuuc
ggguuguaaaguacuuucagcggggaggaagggaguaaaguuaauaccuu
ugcucauugacguuacccgcagaagaagcaccggcuaacuccgugccagc
agccgcgguaauacggagggugcaagcguuaaucggaauuacugggcgua
aagcgcacgcaggcgguuuguuaagucagaugugaaauccccgggcucaa
ccugggaacugcaucugauacuggcaagcuugagucucguagaggggggu
agaauuccagguguagcggugaaaugcguagagaucuggaggaauaccgg
uggcgaaggcggcccccuggacgaagacugacgcucaggugcgaaagcgu
ggggagcaaacaggauuagauacccugguaguccacgccguaaacgaugu
cgacuuggagguugugccggcguggcuuccggagcuaacgcguuaagucg
accgccuggggaguacggccgcaagguuaaaacucaaaugaauugacggg
ggcccgcacaagcgguggagcaugugguuuaauucgaugcaacgcgaaga
accuuaccuggucuugacauccacggaaguuuucagagaugagaaugugc
gaaccgugagacaggugcugcauggcugucgucagcucguguugugaaau
guuggguuaagucccgcaacgagcgcaacccuuauccuuuguugccagcg
guccggccgggaacucaaaggagacugccagugauaaacuggaggaaggu
ggggaugacgucaagucaucauggcccuuacgaccagggcuacacacgug
cuacaauggcgcauacaaagagaagcgaccucgcgagagcaagcggaccu
cauaaagugcgucguaguccggauuggagucugcaacucgacuccaugaa
gucggaaucgcuaguaaucguggaucagaaugccacggugaauacguucc
cgggccuuguacacaccgcccgucacaccaugggaguggguugcaaaaga
aguagguagcuuaaccuucgggagggcgcuuaccacuuugugauucauga
cuggggugaagucguaacaagguaaccguaggggaaccugcgguuggauc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8b0x The translating bacterial ribosome at 1.55 angstrom resolution generated by cryo-EM imaging services.
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): N5 Q6 L7 R9 R12 A13 R14 K15 K18 A26 C27 P28 Q29 R31 K44 N46 S47 A48 L49 R50 K51 T58 Y66 G68 G69 E70 L81 R83 G84 K88 X89 R110 K111 Q112 A113 R114 S115 K116 V119 K120 R121
• Binding residue (residue number reindexed from 1): N4 Q5 L6 R8 R11 A12 R13 K14 K17 A25 C26 P27 Q28 R30 K43 N45 S46 A47 L48 R49 K50 T57 Y65 G67 G68 E69 L80 R82 G83 K87 X88 R109 K110 Q111 A112 R113 S114 K115 V118 K119 R120

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0034336 misfolded RNA binding

Biological Process

• GO:0000372 Group I intron splicing
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0033120 positive regulation of RNA splicing
• GO:0034337 RNA folding
• GO:0046677 response to antibiotic
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8b0x, PDBe:8b0x, PDBj:8b0x
• PDBsum: 8b0x
• PubMed: 36841832
• UniProt: P0A7S3|RS12_ECOLI Small ribosomal subunit protein uS12 (Gene Name=rpsL)