Structure of PDB 7nav Chain D Binding Site BS01

Receptor Information
>7nav Chain D (length=205) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDY
GVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNV
VYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKK
QSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIV
ELYSK
Ligand information
>7nav Chain A (length=1510) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
ucguggaucagaaugccacggugaauacguucccgggccuuguacaccac
caugggaguggguugcaaaagaaguagguagcuuaaccuucgggagggcg
cuuaccacuuugugauucaugacuggggugaaccguaggggaaccugcgg
uuggaucacc
........<<<<..[.((((.>>>>.<<<..<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<...<<.<<<.<<<....>>>.>>>..>>.>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<...<<...
..<<<<........>>>>......>>.......<<<....>>>....<<<
<<<..<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<.
..<<<<<<.........>>>>>>.>>>......>>>..<<<<<<<<....
>>>...>>>>>.>>.<<<<<............>>>>>.<<<<....>>>>
...>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>
>>>..<<<<.......<<<....>>>......>>>>...<.<<<<<....
..<.<<<<<<<<.......>>>>>>>>.>........>>>>>....>..<
<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>
>>.>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<
<<<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>
>...<<<<<<<<...<<<<<<.....<<<<<<<<.....<......>...
.....>>>>>>>>...........<<....>>..>>>>>>..>>>>.>>>
>...>>>...>>>>....<<<<<<...<<...<<<<.........>>>>.
..>>>>>>>>..........<<<<<<..<<<<<<.<<<<<.....>>>>>
.>>>>>>...<<..))>>.....>>>>>>.>>>.<<<.......<<<...
.>>>.....>>>..)))).]<<<<<.<<<<<<<.<<..<<<<...<<<<<
<<<........<<........>>..........<<<<<<<......<<<<
<<<..<<<<<<<....>>>>>>>...<<....>>..>>>>>.>>.<<..<
<<..<<<<<<.<.....<<<<<<<<......>>..<<<<......>>>>.
.>>>>>>.....<<<..<<<<<<....<...<<<.....>>>.>.....>
>>>>>.....<<<<<.....>>>>>.........>>>.....>...>>>.
..>>>>>>.>>...>>>>>>>......>>>>>>>>.....<<<<<<<...
..<<<..<<...<<<....>>>...>>....>>>.....>>>>>>>....
.......<<<<<<<........>>>>>>>...........>>>>.....<
<<<<<<.........>>>>>>>......>>...>>>>>>>>>>.>>...<
<.<<<..<<<<<<<<<<<<....<<<<<<.<<<<..<<....>>.>>>>>
>>>>>...>>>>>>>>>>>>..>>>.>>..<<<<<<<<<....>>>>>>>
>>........
Receptor-Ligand Complex Structure
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PDB7nav A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
Resolution4.8 Å
Binding residue
(original residue number in PDB)		A2 R3 P7 K8 L9 K10 R13 R14 K22 S23 R26 K31 C32 K33 P38 G39 Q40 H41 R44 L48 Y51 L55 Q59 R62 R63 L68 E69 R70 R81 K83 R115 Q116 S119 H120 K121 R128 V130 N131 I132 S134 Y135 Q152 R154 E202 L203 S205 K206
Binding residue
(residue number reindexed from 1)		A1 R2 P6 K7 L8 K9 R12 R13 K21 S22 R25 K30 C31 K32 P37 G38 Q39 H40 R43 L47 Y50 L54 Q58 R61 R62 L67 E68 R69 R80 K82 R114 Q115 S118 H119 K120 R127 V129 N130 I131 S133 Y134 Q151 R153 E201 L202 S204 K205
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0048027 mRNA 5'-UTR binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006353 DNA-templated transcription termination
GO:0006412 translation
GO:0006417 regulation of translation
GO:0031564 transcription antitermination
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0045947 negative regulation of translational initiation
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:7nav, PDBe:7nav, PDBj:7nav
PDBsum7nav
PubMed34088665
UniProtP0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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