Structure of PDB 6ogi Chain Z Binding Site BS01

Receptor Information

>6ogi Chain Z (length=65) Species: 562 (Escherichia coli)

IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAV
KRHAKKLARENARRT

Ligand information

>6ogi 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: 6ogi Extensive ribosome and RF2 rearrangements during translation termination.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R17 R20 E38 K39 R46 A47 K48 S50 R65 R66 T67
• Binding residue (residue number reindexed from 1): R15 R18 E36 K37 R44 A45 K46 S48 R63 R64 T65

Gene Ontology

Molecular Function

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

Biological Process

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

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ogi, PDBe:6ogi, PDBj:6ogi
• PDBsum: 6ogi
• PubMed: 31513010
• UniProt: P68679|RS21_ECOLI Small ribosomal subunit protein bS21 (Gene Name=rpsU)