Structure of PDB 8qoa Chain B Binding Site BS01

Receptor Information

>8qoa Chain B (length=224) Species: 679895 (Escherichia coli BW25113)

VSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEA
LAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTN
WKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKD
MGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGN
DDAIRAVTLYLGAVAATVREGRSQ

Ligand information

>8qoa Chain A (length=1513)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggugcugacgaguggcggacgggugag
uaaugucugggaaacugccugauggagggggauaacuacuggaaacggua
gcuaauaccgcauaacgucgcaagaccaaagaggggccucuugccaucgg
augugcccagaugggauuagcuaguaggugggguaacggcucaccuaggc
gacgaucccuagcuggucugagaggaugaccagccacacuggaacugaga
cacgguccagacuccuacgggaggcagcaguggggaauauugcacaaugg
gcgcaagccugaugcagccaugccgcguguaugaagaaggccuucggguu
guaaaguacuuucagcggggaggaagggaguaaaguuaauaccuuugcuc
auugacguuacccgcagaagaagcaccggcuaacuccgugccagcagccg
cgguaauacggagggugcaagcguuaaucggaauuacugggcguaaagcg
cacgcaggcgguuuguuaagucagaugugaaauccccgggcucaaccugg
gaacugcaucugauacuggcaagcuugagucucguagagggggguagaau
uccagguguagcggugaaaugcguagagaucuggaggaauaccgguggcg
aaggcggcccccuggacgaagacugacgcucaggugcgaaagcgugggga
gcaaacaggauuagauacccugguaguccacgccguaaacgaugucgacu
uggagguugugcccuugaggcguggcuuccggagcuaacgcguuaagucg
accgccuggggaguacggccgcaagguuaaaacucaaaugaauugacggg
ggcccgcacaagcgguggagcaugugguuuaauucgaugcaacgcgaaga
accuuaccuggucuugacauccacggaaguuuucagagaugagaaugugc
cuucgggaaccgugagacaggugcugcauggcugucgucagcucguguug
ugaaauguuggguuaagucccgcaacgagcgcaacccuuauccuuuguug
ccagcgguccggccgggaacucaaaggagacugccagugauaaacuggag
gaagguggggaugacgucaagucaucauggcccuuacgaccagggcuaca
cacgugcuacaauggcgcauacaaagagaagcgaccucgcgagagcaagc
ggaccucauaaagugcgucguaguccggauuggagucugcaacucgacuc
caugaagucggaaucgcuaguaaucguggaucagaaugccacggugaaua
cguucccgggccuuguacacaccgcccgucacaccaugggaguggguugc
aaaagaaguagguagcuuaaccuucgggagggcgcuuaccacuuugugau
ucaugacuggggugaagucguaacaagguaaccguaggggaaccugcggu
uggaucaccuccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qoa SecM adopts alpha-helical conformation in the ribosomal exit tunnel and traps a pre-peptide bond formation state of the ribosome
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R21 W23 P25 K37 R95 G98 G99 T102 N103 K105 T106 K132 R139 I171 K174 E175 N178
• Binding residue (residue number reindexed from 1): R18 W20 P22 K34 R92 G95 G96 T99 N100 K102 T103 K129 R136 I168 K171 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:8qoa, PDBe:8qoa, PDBj:8qoa
• PDBsum: 8qoa
• PubMed: 38503753
• UniProt: P0A7V0|RS2_ECOLI Small ribosomal subunit protein uS2 (Gene Name=rpsB)