Structure of PDB 6ogg Chain J Binding Site BS01

Receptor Information
>6ogg Chain J (length=157) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK
SVEEILG
Ligand information
>6ogg Chain 3 (length=1539) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
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PDB6ogg Extensive ribosome and RF2 rearrangements during translation termination.
Resolution4.2 Å
Binding residue
(original residue number in PDB)		N18 V20 S21 K22 T23 V24 K25 G26 G27 R28 F30 Y49 K51 K61 K65 H88 T89 Q96 A106 G107 R111 L123 K125 A126 S129 N131 R137
Binding residue
(residue number reindexed from 1)		N10 V12 S13 K14 T15 V16 K17 G18 G19 R20 F22 Y41 K43 K53 K57 H80 T81 Q88 A98 G99 R103 L115 K117 A118 S121 N123 R129
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0046677 response to antibiotic
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6ogg, PDBe:6ogg, PDBj:6ogg
PDBsum6ogg
PubMed31513010
UniProtP0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)

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