Structure of PDB 6ogg Chain V Binding Site BS01

Receptor Information

>6ogg Chain V (length=80) Species: 562 (Escherichia coli)

KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNEC
GIGDVVEIRECRPLSKTKSWTLVRVVEKAV

Ligand information

>6ogg Chain 3 (length=1539)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuu
cgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaac
aagguaaccguaggggaaccugcgguuggaucaccuccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ogg Extensive ribosome and RF2 rearrangements during translation termination.
• Resolution: 4.2 Å
• Binding residue (original residue number in PDB): R5 M16 E17 K18 R26 I32 Y33 F36 K38 R39 T41 K42 R64 P65 L66 S67 K68 T69 W72
• Binding residue (residue number reindexed from 1): R3 M14 E15 K16 R24 I30 Y31 F34 K36 R37 T39 K40 R62 P63 L64 S65 K66 T67 W70

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic

Cellular Component

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

External links

• PDB: RCSB:6ogg, PDBe:6ogg, PDBj:6ogg
• PDBsum: 6ogg
• PubMed: 31513010
• UniProt: P0AG63|RS17_ECOLI Small ribosomal subunit protein uS17 (Gene Name=rpsQ)