Structure of PDB 7o5b Chain E Binding Site BS01

Receptor Information

>7o5b Chain E (length=164) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

RIDPSKLELEERLVTVNRVAKVVKGGRRFRFAALVVVGDKNGHVGFGTGK
AQEVPEAIRKAVEDAKKNLIEVPMVGTTIPHEIIGRFGAGNILLKPASEG
TGVIAGGPVRAVLELAGVADILSKSLGSNTPINMIRATLQGLSELKRAED
VAKLRGKSVEELLG

Ligand information

>7o5b Chain A (length=1533)

ggagaguuugauccuggcucaggacgaacgcuggcggcgugccuaauaca
ugcaagucgagcggacagaugggagcuugcucccugauguuagcggcgga
cgggugaguaacacguggguaaccugccuguaagacugggauaacuccgg
gaaaccggggcuaauaccggaugguuguuugaaccgcaugguucaaacau
aaaagguggcuucggcuaccacuuacagauggacccgcggcgcauuagcu
aguuggugagguaacggcucaccaaggcgacgaugcguagccgaccugag
agggugaucggccacacugggacugagacacggcccagacuccuacggga
ggcagcaguagggaaucuuccgcaauggacgaaagucugacggagcaacg
ccgcgugagugaugaagguuuucggaucguaaagcucuguuguuagggaa
gaacaagugccguucgaauagggcgguaccuugacgguaccuaaccagaa
agccacggcuaacuacgugccagcagccgcgguaauacguagguggcaag
cguuguccggaauuauugggcguaaagggcucgcaggcgguuucuuaagu
cugaugugaaagcccccggcucaaccggggagggucauuggaaacugggg
aacuugagugcagaagaggagaguggaauuccacguguagcggugaaaug
cguagagauguggaggaacaccaguggcgaaggcgacucucuggucugua
acugacgcugaggagcgaaagcguggggagcgaacaggauuagauacccu
gguaguccacgccguaaacgaugagugcuaaguguuaggggguuuccgcc
ccuuagugcugcagcuaacgcauuaagcacuccgccuggggaguacgguc
gcaagacugaaacucaaaggaauugacgggggcccgcacaagcgguggag
caugugguuuaauucgaagcaacgcgaagaaccuuaccaggucuugacau
ccucugacaauccuagagauaggacguccccuucgggggcagagugacag
guggugcaugguugucgucagcucgugucgugagauguuggguuaagucc
cgcaacgagcgcaacccuugaucuuaguugccagcauucaguugggcacu
cuaaggugacugccggugacaaaccggaggaagguggggaugacgucaaa
ucaucaugccccuuaugaccugggcuacacacgugcuacaauggacagaa
caaagggcagcgaaaccgcgagguuaagccaaucccacaaaucuguucuc
aguucggaucgcagucugcaacucgacugcgugaagcuggaaucgcuagu
aaucgcggaucagcaugccgcggugaauacguucccgggccuuguacaca
ccgcccgucacaccacgagaguuuguaacacccgaagucggugagguaac
cuuuuaggagccagccgccgaaggugggacagaugauuggggugaagucg
uaacaagguagccguaucggaaggugcggcugg

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7o5b Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp.
• Resolution: 3.33 Å
• Binding residue (original residue number in PDB): V21 A22 K23 V24 V25 G27 R29 R30 K52 K69 F89 A91 S100 I106 A107 R112 L124 S125 K126 S127 L128 S130 N131 T132 N135
• Binding residue (residue number reindexed from 1): V19 A20 K21 V22 V23 G25 R27 R28 K50 K67 F87 A89 S98 I104 A105 R110 L122 S123 K124 S125 L126 S128 N129 T130 N133

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0046677 response to antibiotic

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:7o5b, PDBe:7o5b, PDBj:7o5b
• PDBsum: 7o5b
• PubMed: 35217658
• UniProt: P21467|RS5_BACSU Small ribosomal subunit protein uS5 (Gene Name=rpsE)