Structure of PDB 7aqd Chain E Binding Site BS01

Receptor Information

>7aqd Chain E (length=205) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

PKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKV
KNRSEVRGGGRKPWRQKGTGRARQGSIRSPQWRGGGVVFGPTPRSYSYKL
PKKVRRLAIKSVLSSKVIDNNIIVLEDLTLDTAKTKEMAAILKGLSVEKK
ALIVTADANEAVALSARNIPGVTVVEANGINVLDVVNHEKLLITKAAVEK
VEEVL

Ligand information

>7aqd Chain A (length=2918)

uuaaguuagaaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacgaacaccgauaugcuucggggagcuguaagcaagcuuuga
uccggagauuuccgaauggggaaacccaccacucguaauggagugguauc
cauaucugaauucauaggauaugagaaggcagacccggggaacugaaaca
ucuaaguacccggaggaagagaaagcaaaugcgauucccugaguagcggc
gagcgaaacgggaucagcccaaaccaagaggcuugccucuugggguugua
ggacacucuguacggaguuacaaaggaacgagguagaugaagaggucugg
aaaggcccgccauaggagguaacagcccuguagucaaaacuucguucucu
ccugaguggauccugaguacggcggaacacgugaaauuccgucggaaucc
gggaggaccaucucccaaggcuaaauacucccuagugaccgauagugaac
caguaccgugagggaaaggugaaaagcaccccggaaggggagugaaagag
auccugaaaccgugugccuacaaguagucagagcccguuaacgggugaug
gcgugccuuuuguagaaugaaccggcgaguuacgaucucgugcaagguua
agcagaagaugcggagccgcagcgaaagcgagucugaauagggcgcauga
guacguggucguagacccgaaaccaggugaucuacccauguccaggguga
aguucagguaacacugaauggaggcccgaacccacgcacguugaaaagug
cggggaugagguguggguaggggugaaaugccaaucgaaccuggagauag
cugguucucuccgaaauagcuuuagggcuagccucaagguaagagucuug
gagguagagcacugauuggacuaggggccccuaccggguuaccgaauuca
gucaaacuccgaaugccaaugacuuauccuugggagucagacugcgagug
auaagauccguagucgaaagggaaacagcccagaccgccagcuaaggucc
caaaguauacguuaaguggaaaaggauguggaguugcuuagacaaccagg
auguuggcuuagaagcagccaccauuuaaagagugcguaauagcucacug
gucgagugacucugcgccgaaaauguaccggggcuaaacguaucaccgaa
gcugcggacuguucuucgaacagugguaggagagcguucuaagggcugug
aagccagaccggaaggacugguggagcgcuuagaagugagaaugccggua
ugaguagcgaaagaggggugagaauccccuccaccgaaugccuaagguuu
ccugaggaaggcucguccgcucaggguuagucgggaccuaagccgaggcc
gaaaggcguaggcgauggacaacagguugauauuccuguaccaccuccuc
accauuugagcaauggggggacgcaggaggauaggguaagcgcgguauug
gauauccgcguccaagcaguuaggcugggaaauaggcaaauccguuuccc
auaagccugagcugugauggcgagcgaaauauaguagcgaaguuccugau
uccacacugccaagaaaagccucuagcgaggugagaggugcccguaccgc
aaaccgacacagguaggcgaggagagaauccuaaggugaucgagagaacu
cucguuaaggaacucggcaaaaugaccccguaacuucgggagaaggggug
cucuguuagggugcaagcccgagagagccgcagugaauaggcccaggcga
cuguuuagcaaaaacacaggucucugcgaagccguaaggcgaaguauagg
ggcugacgccugcccggugcuggaagguuaagaggagcgcuuagcguaag
cgaaggugcgaauugaagccccaguaaacggcggccguaaacgguccuaa
gguagcgaaauuccuugucggguaaguuccgacccgcacgaaaggcgcaa
cgaucugggcacugucucaacgagagacucggugaaauuauaguaccugu
gaagaugcagguuacccgcgacaggacggaaagaccccguggagcuuuac
ugcagccugauauugaauguugguacagcuuguacaggauagguaggagc
cuuggaaaccggagcgccagcuucgguggaggcaucggugggauacuacc
cuggcuguauugaccuucuaacccgccgcccuuaucgggcggggagacag
ugucaggugggcaguuugacuggggcggucgccuccuaaaagguaacgga
ggcgcccaaagguucccucagaaugguuggaaaucauucgcagaguguaa
aggcacaagggagcuugacugcgagaccuacaagucgagcagggacgaaa
gucgggcuuagugauccggugguuccgcauggaagggccaucgcucaacg
gauaaaagcuaccccggggauaacaggcuuaucucccccaagaguccaca
ucgacggggagguuuggcaccucgaugucggcucaucgcauccuggggcu
guagucggucccaaggguugggcuguucgcccauuaaagcgguacgcgag
cuggguucagaacgucgugagacaguucggucccuauccgucgcgggcgc
aggaaauuugagaggagcuguccuuaguacgagaggaccgggauggacgc
accgcugguguaccaguuguucugccaagggcaucgcuggguagcuaugu
gcggacgggauaagugcugaaagcaucuaagcaugaagccccccucaaga
ugagauuucccauuccgcaaggaaguaagaucccugaaagaugaucaggu
ugauaggucugagguggaaguguggcgacacauggagcugacagauacua
aucgaucgaggacuuaac

<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<.....
.<<<<<<.....((.>>>.....<<<<<<<..<<<)).....>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<<.....<<....
>>......>>>>>.>.........<<....>>...<<<<......<<...
..>>.....>>>>...(((....<<<<<<<<<..>>>>>>>>>......<
<<<<<<<<.....<<<<.......<<<<<<<<<<.<<<.....<<<<...
...>>>>.((......<<<.....))>>>...>>>...>>>>>>>>>>>>
>>.>>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......
<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]]..........
.....<<....>>....]].........<<<<....>>>>..........
...}....>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>
>>...<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<..
.<<<.....>>>...>>>...<<....>>..<<<<.....>>>>......
>>>>>.>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<<..
.<<<<<<......>>>>>>...>.>>>...<<<.<<<<<........>>>
>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>...>..
>.>>..<<<<<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<
<.....<<<...<<<<<<<<...<<.<<<<.....>>>>..>>...>>>>
>>>>..>>.>.....>>>>.>>>>>..>>>>>>>.>>..<<<<<<<.<<.
.....>>.>>>>>>>....<<<......>>>...<<<<.<<<...<<<((
(.....<<<<<<...........<<..<<<<<<<<<........<<<<<.
<<...<<<<.......>>>>...>>.........<<......>>...>>>
>>....>>>>>>>>>.>>...........))).....>>>>>>.>>>...
>>>>>>><<<<<<<...>>>>>>>....>>>>>>..<<<<<<<.<<....
..<<<<<.<<....>>.>>>>>...>>.>>>>>>>........>>>>>><
......<<....<<<<<<.......>>>>>><<<<....<<<<<.<<...
<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<
....>>>...>>>...>>...<<<<<........>>>>>))<<<<<.<<<
<<<......<<...<<<<....<<<<..<<<..<<<.<.<<<.<.....{
....>.>>>.<<..<..<<<<<<<<.<<<<<<..<<.....>>.>>>>>>
....>>>>>.>>>.>...>><..<<...........>>...>>.>>>...
>>>...>>>>.........>>>>..>>..>>>>>>>>>>>>>>>..>>..
...<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<
<<<<<<.<<<..............<<<<<.....<..>......>>>>><
<<<<....<<<<....>>>>...>>>>>............<<<<<<<<<.
.<<<.........>>>..<<<<<<<.....<<<....>>>.......>>>
>>>>..<<<<.<<<..<<<<<<<..<<<...<<...<<<<<<.<<....>
>..>>>>>>...>>...>>>>>>>>..>>>>><<<<<<..>>>>>>....
....<...........<<<<<<.....>>>>>>.....>....>>>>...
>>.>>>>>>>....>>>.>>>>>>>>.>>>>>>.....>.(...<<<<<.
......)>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<<<..<<
<<<.<<<<<<<<<.<<<.<<<<<<<<<<<<...........<<<<<..<<
<......<<<<<<<<....>>>>>>>>...>>>............>>>>>
..>>>>>>>>>>>>.>>>....<<.<<<<<<.....>>>>>>>>.....>
>>>>>>>>..>>>>>..<<<<.....>>>><<<<<<...........>>>
>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(
((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....
>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>>>.......
......>>>>..]]>>>>.......<<<<.<.<<<<<<...<<.......
>>...>>>>>>...>>>>.>.......<<<<<.<<<<<<..<<<<<<<<<
......>>>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>
>>.>>....<<<<<<<....>>>.>>>>....]]..)))>>>>>>>>...
.<<<<<<<...<<<<..<<<<<<<...............>>>>>>>.<<<
<<...<<<<...<<<<<<<<<<<.}..>>>>>>..>>>>>...>>>>.>>
>>>...<<<....<<<<<...........>>>>>....>>>.>>>>....
...>>>>>>>..<<<<....>>>>....<<<<<<<<<.......>>>>>.
...<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>
...>>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7aqd Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): L38 M39 Q40 R41 S43 L44 R45 Q46 T48 H49 K50 V51 K52 N53 R54 S55 V57 R58 G60 R62 K63 Q67 K68 G69 G71 R72 A73 R74 Q75 G76 R79 P81 Q82 W83 R84 V88 F90 G91 P92 R95 Y99 K103 K104 V105 R106 R107 A134 K135 T136 K137 K151 L165 R168 N169 G180
• Binding residue (residue number reindexed from 1): L37 M38 Q39 R40 S42 L43 R44 Q45 T47 H48 K49 V50 K51 N52 R53 S54 V56 R57 G59 R61 K62 Q66 K67 G68 G70 R71 A72 R73 Q74 G75 R78 P80 Q81 W82 R83 V87 F89 G90 P91 R94 Y98 K102 K103 V104 R105 R106 A133 K134 T135 K136 K150 L164 R167 N168 G179

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7aqd, PDBe:7aqd, PDBj:7aqd
• PDBsum: 7aqd
• PubMed: 33259811
• UniProt: P42921|RL4_BACSU Large ribosomal subunit protein uL4 (Gene Name=rplD)