Structure of PDB 6q9a Chain 5 Binding Site BS01

Receptor Information

>6q9a Chain 5 (length=118) Species: 562 (Escherichia coli)

IALNKRARHEYFIEEEFEAGLALQGWEVKSLRAGKANISDSYVLLRDGEA
FLFGANITPMAVASTHVVCDPTRTRKLLLNQRELDSLYGRVNREGYTVVA
LSLYWKNAWCKVKIGVAK

Ligand information

>6q9a Chain 2 (length=1534)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccu
ucgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaa
caagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q9a How a circularized tmRNA moves through the ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): N17 K18 R19 K48 A49 S52
• Binding residue (residue number reindexed from 1): N4 K5 R6 K35 A36 S39

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

External links

• PDB: RCSB:6q9a, PDBe:6q9a, PDBj:6q9a
• PDBsum: 6q9a
• PubMed: 30765567
• UniProt: P0A832|SSRP_ECOLI SsrA-binding protein (Gene Name=smpB)