Structure of PDB 8syl Chain b Binding Site BS01

Receptor Information

>8syl Chain b (length=224) Species: 562 (Escherichia coli)

VSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEA
LAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTN
WKTVRQSIKRLKDLETQSQDGTFEKLTKKEALMRTRELEKLENSLGGIKD
MGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGN
DDAIRAVTLYLGAVAATVREGRSQ

Ligand information

>8syl Chain a (length=1528)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugccggcguggcuu
ccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaagguu
aaaacucaaaugaauugacgggggcccgcacaagcgguggagcauguggu
uuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacggaa
guuuucagagaugagaaugugccuucgggaaccgugagacaggugcugca
uggcugucgucagcucguguugugaaauguuggguuaagucccgcaacga
gcgcaacccuuauccuuuguugccagcgguccggccgggaacucaaagga
gacugccagugauaaacuggaggaagguggggaugacgucaagucaucau
ggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaagag
aagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccgg
auuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgug
gaucagaaugccacggugaauacguucccgggccuuguacacaccgcccg
ucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucggg
agggcgcuuaccacuuugugauucaugacuggggugaagucguaacaagg
uaaccguaggggaaccugcgguuggauc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8syl Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R21 W23 P25 R95 L97 G98 G99 T102 N103 K105 T106 I171 E175 N178
• Binding residue (residue number reindexed from 1): R18 W20 P22 R92 L94 G95 G96 T99 N100 K102 T103 I168 E172 N175

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8syl, PDBe:8syl, PDBj:8syl
• PDBsum: 8syl
• PubMed: 37537169
• UniProt: P0A7V0|RS2_ECOLI Small ribosomal subunit protein uS2 (Gene Name=rpsB)