Structure of PDB 8p5d Chain SQ0 Binding Site BS01

Receptor Information

>8p5d Chain SQ0 (length=142) Species: 1358809 (Spraguea lophii 42_110)

SIAQVITKGTRKTAISKCVCSESNEFQLMVDNMTLDVHHDNFLVAKIKEI
MKIIGYEHLENLKFELTTRGGGPISRAYAIRQAFAKAVISYFGKYYDEQR
KQDIKEQIMKFDRAALVADPRRVEPKKYGGPAARAKYTKSYR

Ligand information

>8p5d Chain S60 (length=1354)

accagguugauucugccugacguggaugcuagucucauagauuuagccau
gcauguguaagcgaagcgauuagugaagcggcggaaggcucaguaacggg
cgaguauuuaaucucuagaaccggacaaccucaggaaacagaggggaaaa
cggaguaagagcauguguuagcaugugaugagaacaacagugcaggagag
uaagaagccaucccaucaguuaguaaguaggguaagggccuauuuagacg
uagacggguacgggggauuaggguuugauuccggagagggagccugagag
acggcuaccagguccaaggacagcagcaggcgcgaaaauuaccgaagccu
ccaagagggcgguagugaagagacgugaaaacaaguguguguaaaaacca
caugaguaacuggaggucaaggcuggugccagcauccgcgguaauaccag
cuccaggagugucuaugaugauugcugcgauuaaaagguccguagucgaa
gaacaguacuuguuuguaauguggcuuaucgagagccgaauagaacgaga
agaguucagaguaaggagcgaaggagggcuagauuauugagcagcgagag
gugaaauuugaugaccugcuuaggaguaacagaggcgaaagcgcuaguca
agaacgaauccgaugaucaaggacguaggcuggaggaucgaagacgauua
gagaccguaguaguuccagcaguaaacgaugccuacgcuguugugguuau
gagcacggcagaagagaaaucuaguagggcuuuggggagaguacgcgcgc
aagcgauaaauuuaaaggaaauugacggaagaacaccacaaggaguggag
ugugcggcuuaauuugacucaacgcgggacagcuuaccauacccgauggc
cgugugagcguaguacgcgauaggucagagaguggugcauggccguuaac
gacgaguggggugaccuuuggguuaaguccgcgaaguagugagaucccua
ggauacgaaaguuaucgacagguguuaaaaacacaggaaggaaggggcaa
gaacaggucagugaugcccuuagaugguaugggcugcacgcgcacuacag
uggucacagcagaaacaaauagaaguaaaugugaucgagagggaaugagc
acuguaaugugcacaggaacgaggaauugcuaguaaucguuaucucauua
agaagcgaugaaugugucccuguucuuuguacacaccgcccgucguuauc
gaagauggaaccaggugcgaacaagugaaagcgagugagugcaggguucu
agaucugauacaagucguaacaaggcagcuguaggagaaccuguagcugg
auca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p5d Spraguea lophii ribosome
• Resolution: 10.8 Å
• Binding residue (original residue number in PDB): R12 K13 T14 R70 G72 G73 P74 I75 S76 R77 R114 P121 R122 R123 V124 E125 K127 K128 Y129 A133 A134 R135 A136 K137 T139 K140 Y142
• Binding residue (residue number reindexed from 1): R11 K12 T13 R69 G71 G72 P73 I74 S75 R76 R113 P120 R121 R122 V123 E124 K126 K127 Y128 A132 A133 R134 A135 K136 T138 K139 Y141

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8p5d, PDBe:8p5d, PDBj:8p5d
• PDBsum: 8p5d
• PubMed: 37709902
• UniProt: S7WDU9