Structure of PDB 7y7d Chain D Binding Site BS01

Receptor Information

>7y7d Chain D (length=205) Species: 562 (Escherichia coli)

ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDY
GVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNV
VYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKK
QSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIV
ELYSK

Ligand information

>7y7d Chain A (length=1520)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggccucuugccaucggaugugcccagaugggauuagcuaguagguggg
guaacggcucaccuaggcgacgaucccuagcuggucugagaggaugacca
gccacacuggaacugagacacgguccagacuccuacgggaggcagcagug
gggaauauugcacaaugggcgcaagccugaugcagccaugccgcguguau
gaagaaggccuucggguuguaaaguacuuucagcggggaggaagggagua
aaguuaauaccuuugcucauugacguuacccgcagaagaagcaccggcua
acuccgugccagcagccgcgguaauacggagggugcaagcguuaaucgga
auuacugggcguaaagcgcacgcaggcgguuuguuaagucagaugugaaa
uccccgggcucaaccugggaacugcaucugauacuggcaagcuugagucu
cguagagggggguagaauuccagguguagcggugaaaugcguagagaucu
ggaggaauaccgguggcgaaggcggcccccuggacgaagacugacgcuca
ggugcgaaagcguggggagcaaacaggauuagauacccugguaguccacg
ccguaaacgaugucgacuuggagguugugccggcguggcuuccggagcua
acgcguuaagucgaccgccuggggaguacggccgcaagguuaaaacucaa
augaauugacgggggcccgcacaagcgguggagcaugugguuuaauucga
ugcaacgcgaagaaccuuaccuggucuugacauccacggaaguuuucaga
gaugagaaugugccuucgggaaccgugagacaggugcugcauggcugucg
ucagcucguguugugaaauguuggguuaagucccgcaacgagcgcaaccc
uuauccuuuguugccagcgguccggccgggaacucaaaggagacugccag
ugauaaacuggaggaagguggggaugacgucaagucaucauggcccuuac
gaccagggcuacacacgugcuacaauggcgcauacaaagagaagcgaccu
cgcgagagcaagcggaccucauaaagugcgucguaguccggauuggaguc
ugcaacucgacuccaugaagucggaaucgcuaguaaucguggaucagaau
gccacggugaauacguucccgggccuuguacacaccgcccgucacaccau
gggaguggguugcaaaagaaguagguagcuuaaccuucgggagggcgcuu
accacuuugugauucaugacuggggugaagucguaacaagguaaccguag
gggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7y7d Glycosylation of queuosine in tRNAs contributes to optimal translation and post-embryonic growth in vertebrates (Under submission)
• Resolution: 2.58 Å
• Binding residue (original residue number in PDB): A2 R3 L5 P7 L9 K10 R13 R14 K22 S23 R26 K31 C32 P38 G39 H41 Y51 L55 R56 K58 Q59 R62 L68 E69 R70 N74 R81 T110 E113 R115 S119 H120 V130 N131 I132 S134 Y135 R146 K148 Q152 E202 K206
• Binding residue (residue number reindexed from 1): A1 R2 L4 P6 L8 K9 R12 R13 K21 S22 R25 K30 C31 P37 G38 H40 Y50 L54 R55 K57 Q58 R61 L67 E68 R69 N73 R80 T109 E112 R114 S118 H119 V129 N130 I131 S133 Y134 R145 K147 Q151 E201 K205

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

External links

• PDB: RCSB:7y7d, PDBe:7y7d, PDBj:7y7d
• PDBsum: 7y7d
• PubMed: 37992713
• UniProt: P0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)