Structure of PDB 7zjx Chain LS Binding Site BS01

Receptor Information

>7zjx Chain LS (length=159) Species: 9986 (Oryctolagus cuniculus)

VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLKKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKEQIVPKP

Ligand information

>7zjx Chain L5 (length=3732)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcgguggggcgcgggaaau
guggcguacggaagacccacuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcgugguccggccgugccggcg
gucucggcggaucuuucccgcuccggggucggcgggggaccgccccccgg
ccggcgaccggccgccgccgggcgcauuuccaccgcggcggugcgccgcg
accggcuccgggacggcugggaaggccccggcggggaagguggcccgggg
ggacgccucgccggcgggcgcgaccccuccccggguguuacagccccgcc
ccggcagcagcagcucgccgaaucccggggccgagggagcgagaccugug
ucgccgcgcucuccccccucgggggggccgggccgccccucccacggcgc
gaccgcucggggcggacuguccccagugcgccccgggcgugucacgccgu
cgggcucgggggaggccacggcgcgucgcgcgccggcgcgcgcgcgcgag
cgagcgcacggggucggcggcgaugucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcggcggcgccgucgucg
gccgaggugggaucccgaggcccuuccaguccgccgagggcgcaccaccg
gcccgucucgcccgccgcgccggggagguggagcacgagcgcacguguua
ggacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaa
cucugguggagguccguagcgguccugacgugcaaaucggucguccgacc
uggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccuc
cgaaguuucccucaggauagcuggcgcucucgcaaccccgcaguuuuauc
cgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuau
ucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccggg
cguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgc
ugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucauc
agaccccagaaaagguguugguugauauagacagcaggacgguggccaug
gaagucggaauccgcuaaggaguguguaacaacucaccugccgaaucaac
uagcccugaaaauggauggcgcuggagcgucgggcccauacccggccguc
gcuggcagucggcagagcgagaaagagaguggagccgcggacgcuacgcc
gcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcggg
cccggguggagccgccgcaggugcagaucuuggugguaguagcaaauauu
caaacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagc
aguugaacaugggucagucgguccugagagaugggcgagcgccguuccga
agggacgggcgauggccuccguugcccucagccgaucgaaagggagucgg
guucagauccccgaauccggaguggcggagaugggcgccgcgaggcgucc
agugcgguaacgcgaccgaucccggagaagccggcgggagccccggggag
aguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcccc
gagagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgg
ugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgc
gccgggccguacccauauccgcagcaggucuccaaggugaacagccucug
gcauguuggaacaauguagguaagggaagucggcaagccggauccguaac
uucgggauaaggauuggcucuaagggcugguagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuau
gacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggaugaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaagagacaugagagguguagaau
aagugggaggcccgggccgccggugaaauaccacuacucuuaucguuuuu
ucacugacccggugaggcgggggggcgagccccgaggggcucucgcuucu
ggcgccaagcgccgggccccgucgguccgggccggcggcggccgggcgcg
acccgcuccggggacagugccagguggggaguuugacuggggcgguacac
cugucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaa
accucccguggagcagaagggcaaaagcucgcuugaucuugauuuucagu
acgaauacagaccgugaaagcggggccucacgauccuucugagcuuuugg
guuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugu
ggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggc
ucuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugauguguuguugccaugguaauccugcucaguacgag
aggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaa
uggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucag
aaucccgcccaggcggaacgauacggcagcgccgaaggagccucgguugg
ccucggauagccggucccccgcgggguccggugcggagagcccuucgucc
cgggaaauggggcgcggccggaaagggggccgcccucucgcccgucacgc
accgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugc
uucugggucgggguuucguacguagcagagcagcucccucgcugcgaucu
auugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7zjx Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): V2 R3 Y4 L6 K16 S17 R18 S20 R23 H25 F26 K27 R30 Q34 K37 K43 K46 K54 K55 R62 Y63 G65 G66 G68 R69 A71 Q72 K74 Q75 W78 Q80 R82 W83 P84 K85 K86 H93 K96 N97 S100 N101 L104 Q118 V119 K121 R127 Y130 R131 A132 H133 G134 R135 I136 N137 P138 Y139 M140 S141
• Binding residue (residue number reindexed from 1): V1 R2 Y3 L5 K15 S16 R17 S19 R22 H24 F25 K26 R29 Q33 K36 K42 K45 K53 K54 R61 Y62 G64 G65 G67 R68 A70 Q71 K73 Q74 W77 Q79 R81 W82 P83 K84 K85 H92 K95 N96 S99 N100 L103 Q117 V118 K120 R126 Y129 R130 A131 H132 G133 R134 I135 N136 P137 Y138 M139 S140

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7zjx, PDBe:7zjx, PDBj:7zjx
• PDBsum: 7zjx
• PubMed: 35709277
• UniProt: A0A8J4KQ25